ClinVar Genomic variation as it relates to human health
NM_201631.4(TGM5):c.337G>T (p.Gly113Cys)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_201631.4(TGM5):c.337G>T (p.Gly113Cys)
Variation ID: 6039 Accession: VCV000006039.50
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 15q15.2 15: 43260151 (GRCh38) [ NCBI UCSC ] 15: 43552349 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Nov 10, 2014 Dec 22, 2024 Jul 8, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_201631.4:c.337G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_963925.2:p.Gly113Cys missense NM_004245.4:c.190+249G>T intron variant NC_000015.10:g.43260151C>A NC_000015.9:g.43552349C>A NG_016124.1:g.11707G>T O43548:p.Gly113Cys - Protein change
- G113C
- Other names
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- Canonical SPDI
- NC_000015.10:43260150:C:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00140 (A)
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Allele frequency
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The frequency of the allele represented by this VCV record.
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1000 Genomes Project 30x 0.00109
1000 Genomes Project 0.00140
Trans-Omics for Precision Medicine (TOPMed) 0.00202
The Genome Aggregation Database (gnomAD), exomes 0.00235
The Genome Aggregation Database (gnomAD) 0.00252
Exome Aggregation Consortium (ExAC) 0.00260
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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TGM5 | - | - |
GRCh38 GRCh37 |
165 | 187 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (8) |
criteria provided, multiple submitters, no conflicts
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Jul 8, 2024 | RCV000006411.22 | |
Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Jun 22, 2023 | RCV000340380.28 | |
TGM5-related disorder
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Pathogenic (1) |
criteria provided, single submitter
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Jun 9, 2023 | RCV003398452.4 |
Pathogenic (1) |
criteria provided, single submitter
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Oct 3, 2016 | RCV000623924.4 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(May 04, 2022)
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criteria provided, single submitter
Method: clinical testing
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Acral peeling skin syndrome
Affected status: unknown
Allele origin:
germline
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Mendelics
Accession: SCV002519866.1
First in ClinVar: May 28, 2022 Last updated: May 28, 2022 |
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Pathogenic
(Oct 03, 2016)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: yes
Allele origin:
germline
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Ambry Genetics
Accession: SCV000741601.3
First in ClinVar: Apr 15, 2018 Last updated: Jan 07, 2023 |
Number of individuals with the variant: 1
Clinical Features:
Eczema (present) , Abnormal blistering of the skin (present) , Allergy (present)
Sex: male
Ethnicity/Population group: Unknown
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Pathogenic
(Oct 17, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: not provided
Allele origin:
germline
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Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Accession: SCV004026188.1
First in ClinVar: Aug 19, 2023 Last updated: Aug 19, 2023 |
Comment:
PM3, PS3, PP4, PP3, PS4
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Pathogenic
(Oct 07, 2021)
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criteria provided, single submitter
Method: clinical testing
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Acral peeling skin syndrome
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002018966.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Jun 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001249030.27
First in ClinVar: May 12, 2020 Last updated: Dec 22, 2024 |
Comment:
TGM5: PM3:Very Strong, PM2:Supporting, PP4, PS3:Supporting
Number of individuals with the variant: 3
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Pathogenic
(Oct 18, 2017)
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criteria provided, single submitter
Method: clinical testing
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Acral peeling skin syndrome
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000391245.3
First in ClinVar: Dec 06, 2016 Last updated: May 24, 2019 |
Comment:
Across a selection of the available literature, the TGM5 c.337G>T (p.Gly113Cys) missense variant, which is a founder variant in the European population, was reported in … (more)
Across a selection of the available literature, the TGM5 c.337G>T (p.Gly113Cys) missense variant, which is a founder variant in the European population, was reported in at least 97 patients, including in a homozygous state in at least 91 patients with peeling skin syndrome, in a compound heterozygous state in at least six patients, and in a heterozygous state in six unaffected parents of patients (Cassidy et al. 2005; Kiritsi et al. 2010; van der Velden et al. 2012; Pigors et al. 2012; Kavaklieva et al. 2013; Szczecinska et al. 2014; KopeÄková et al. 2016). The variant was identified in a heterozygous state in four out of 250 controls and is reported at a frequency of 0.00454 in the European American population of the Exome Sequencing Project. This frequency is higher than expected based on disease prevalence estimates, but may be consistent with under-diagnosis and with the fact that this is a common founder variant. Cassidy et al. (2005) measured enzyme activity for the p.Gly113Cys variant in two different epithelial cell lines and demonstrated that the variant completely abolished activity. Based on the collective evidence, the p.Gly113Cys variant is classified as pathogenic for peeling skin syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. (less)
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Pathogenic
(Mar 08, 2021)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000329549.6
First in ClinVar: Dec 06, 2016 Last updated: Apr 17, 2019 |
Comment:
Common variant identified especially in individuals of Northern European descent (Lek et al., 2016); Published functional studies demonstrate that G113C completely abolishes cross-linking activity of … (more)
Common variant identified especially in individuals of Northern European descent (Lek et al., 2016); Published functional studies demonstrate that G113C completely abolishes cross-linking activity of the enzyme in transfected epithelial cell lines (Cassidy et al., 2005; van der Velden et al., 2015); This variant is associated with the following publications: (PMID: 16380904, 24019772, 27206604, 26707537, 30688214, 31028847, 20301543, 20220177, 19440220, 22622422, 25510201, 26684698, 22429841, 24628291, 29242947, 31001817, 31980526, 25644735, 20164844, 31589614) (less)
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Pathogenic
(Nov 01, 2021)
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criteria provided, single submitter
Method: clinical testing
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Acral peeling skin syndrome
Affected status: yes
Allele origin:
germline
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Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
Accession: SCV002061667.2
First in ClinVar: Jan 22, 2022 Last updated: Feb 11, 2022 |
Comment:
PM3_strong, PS3, PP1, PP3
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Pathogenic
(Jun 09, 2023)
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criteria provided, single submitter
Method: clinical testing
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TGM5-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004105253.1
First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023 |
Comment:
The TGM5 c.337G>T variant is predicted to result in the amino acid substitution p.Gly113Cys. This variant, in either the homozygous or compound heterozygous states with … (more)
The TGM5 c.337G>T variant is predicted to result in the amino acid substitution p.Gly113Cys. This variant, in either the homozygous or compound heterozygous states with a second pathogenic variant, has been reported to be causative for acral peeling skin syndrome in multiple unrelated families (Cassidy et al. 2005. PubMed ID: 16380904; Kiritsi et al. 2010. PubMed ID: 20164844; Pigors et al. 2012. PubMed ID: 22622422; Kavaklieva et al. 2013. PubMed ID: 24019772; van der Velden et al 2015. PubMed ID: 25644735; Has et al. 2018. PubMed ID: 29242947). This variant is interpreted as pathogenic. (less)
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Pathogenic
(Jul 17, 2023)
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criteria provided, single submitter
Method: clinical testing
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Acral peeling skin syndrome
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002768500.2
First in ClinVar: Dec 24, 2022 Last updated: Jul 23, 2024 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease … (more)
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene and is associated with peeling skin syndrome 2 (MIM#609796). (I) 0106 - This gene is known to be associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from glycine to cysteine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (657 heterozygotes, 2 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated N-terminal transglutaminase domain (NCBI). (I) 0705 - No comparable variants have previous evidence for pathogenicity. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported as homozygous and compound heterozygous in individuals with peeling skin syndrome (ClinVar, PMID: 29242947). (SP) 1002 - Moderate functional evidence supporting abnormal protein function. Transfected cell lines displayed complete loss of enzyme activity (PMID: 16380904). (SP) 1208 - Inheritance information for this variant is not currently available. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Pathogenic
(Jun 22, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics Laboratory, Skane University Hospital Lund
Accession: SCV005198783.1
First in ClinVar: Aug 25, 2024 Last updated: Aug 25, 2024 |
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Pathogenic
(Jul 08, 2024)
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criteria provided, single submitter
Method: clinical testing
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Acral peeling skin syndrome
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
unknown
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Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV005368343.1
First in ClinVar: Oct 13, 2024 Last updated: Oct 13, 2024 |
Comment:
Criteria applied: PM3_VSTR,PS3_SUP,PP3
Clinical Features:
Abnormal blistering of the skin (present)
Sex: female
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Pathogenic
(Oct 01, 2012)
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no assertion criteria provided
Method: literature only
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PEELING SKIN SYNDROME 2
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000026594.2
First in ClinVar: Apr 04, 2013 Last updated: Nov 10, 2014 |
Comment on evidence:
Cassidy et al. (2005) described a homozygous missense mutation in exon 3 of the TGM5 gene in members of 2 unrelated families, 1 Dutch and … (more)
Cassidy et al. (2005) described a homozygous missense mutation in exon 3 of the TGM5 gene in members of 2 unrelated families, 1 Dutch and 1 Scottish, who suffered from an acral form of peeling skin syndrome (PSS2; 609796). A gly113-to-cys (G113C) mutation arose from a c.337G-T transversion. In fact, 2 homozygous missense mutations were found; functional analysis in 2 different cell lines demonstrated that one was a rare polymorphism that did not significantly reduce TGM5 activity, whereas the G113C mutant, which completely abolished crosslinking activity, was the pathogenic change. In 6 unrelated children and 1 adult patient from Germany and a 1-year-old child from Finland with blistering and peeling acral skin, Kiritsi et al. (2010) identified homozygosity for the G113C mutation in the TGM5 gene. In a 2-year-old Swedish child, they detected compound heterozygosity for G113C and a c.763T-C transition in TGM5 that resulted in a trp255-to-arg substitution (W255R; 603805.0003) at a conserved residue within the core domain close to the catalytic site. Immunofluorescence staining of patient skin demonstrated that mutant TGM5 was restricted to a few cell layers compared to wildtype. In addition, loricrin (LOR; 152445), involucrin (IVL; 147360), and filaggrin (FLG; 135940) were all distributed more diffusely in patient skin samples compared to controls. In 6 patients from 6 unrelated families with acral peeling skin syndrome, van der Velden et al. (2012) identified homozygosity for the G113C mutation in the TGM5 gene, as well as homozygosity for the T109M polymorphism. Genealogic research dating to the year 1650 revealed no consanguinity between the families. Haplotype analysis of these 6 families, including 5 from the Netherlands and 1 from Germany, as well as of the 2 Dutch and Scottish families previously studied by Cassidy et al. (2005), revealed that all mutation carriers were homozygous for an approximately 0.16-Mb region that begins centromeric of and includes the TGM5 gene. Van der Velden et al. (2012) noted that in contrast to the 2 Tunisian patients (603805.0002) reported by Kharfi et al. (2009), all 21 reported European acral peeling skin syndrome patients carried the G113C mutation linked to the T109M variant, suggesting an ancestral founder mutation in the European population. In 7 patients with acral peeling skin syndrome, including 4 Germans, 1 Spaniard, 1 Slovakian, and 1 Hungarian, Pigors et al. (2012) identified homozygosity for the G113C substitution in the TGM5 gene. In addition, 2 German patients were compound heterozygous for G113C and another mutation in TGM5: a 7-year-old patient also carried a c.122T-C transition in exon 2, resulting in a leu41-to-pro substitution (L41P; 603805.0004) that was not found in 100 controls; and a 12-year-old patient carried a 1-bp deletion in TGM5 (640delC; 603805.0005) on the second TGM5 allele. The unaffected parents from 3 families were available for study, and each was heterozygous for 1 of the mutations carried by their offspring. Functional analysis in patient keratinocytes demonstrated a decrease in TGase activity at the pH optimal for TGM5; in addition, there was upregulation of the TGM5 substrates LOR and IVL as well as of KRT1 (139350), KRT10 (148080), and corneodesmosin (CDSN; 602593) in patient keratinocytes compared to controls. (less)
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not provided
(-)
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no classification provided
Method: literature only
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Acral peeling skin syndrome
Affected status: yes
Allele origin:
germline
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GeneReviews
Accession: SCV000322809.2
First in ClinVar: Oct 11, 2015 Last updated: Oct 01, 2022 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Epidermolysis Bullosa Simplex. | Adam MP | - | 2022 | PMID: 20301543 |
The Position of Targeted Next-generation Sequencing in Epidermolysis Bullosa Diagnosis. | Has C | Acta dermato-venereologica | 2018 | PMID: 29242947 |
Ten years of DNA diagnostics of epidermolysis bullosa in the Czech Republic. | Kopečková L | The British journal of dermatology | 2016 | PMID: 26707537 |
Under-recognition of acral peeling skin syndrome: 59 new cases with 15 novel mutations. | Szczecinska W | The British journal of dermatology | 2014 | PMID: 24628291 |
Acral peeling skin syndrome resembling epidermolysis bullosa simplex in a 10-month-old boy. | Kavaklieva S | Case reports in dermatology | 2013 | PMID: 24019772 |
TGM5 mutations impact epidermal differentiation in acral peeling skin syndrome. | Pigors M | The Journal of investigative dermatology | 2012 | PMID: 22622422 |
A recurrent mutation in the TGM5 gene in European patients with acral peeling skin syndrome. | van der Velden JJ | Journal of dermatological science | 2012 | PMID: 22036214 |
Acral peeling skin syndrome with TGM5 gene mutations may resemble epidermolysis bullosa simplex in young individuals. | Kiritsi D | The Journal of investigative dermatology | 2010 | PMID: 20164844 |
A missense mutation in TGM5 causes acral peeling skin syndrome in a Tunisian family. | Kharfi M | The Journal of investigative dermatology | 2009 | PMID: 19440220 |
A homozygous missense mutation in TGM5 abolishes epidermal transglutaminase 5 activity and causes acral peeling skin syndrome. | Cassidy AJ | American journal of human genetics | 2005 | PMID: 16380904 |
Text-mined citations for rs112292549 ...
HelpRecord last updated Dec 22, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.