VCV001710134.3 - ClinVar

NM_007129.5(ZIC2):c.1213_1216delinsGCATGT (p.Pro405fs)

Germline

Classification

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.

(3)

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.

Likely pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_007129.5(ZIC2):c.1213_1216delinsGCATGT (p.Pro405fs)

Variation ID: 1710134 Accession: VCV001710134.3

Type and length

Indel, 6 bp

Location

Cytogenetic: 13q32.3 13: 99985083-99985086 (GRCh38) [ NCBI UCSC ] 13: 100637337-100637340 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	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	Oct 15, 2022	Jun 17, 2023	Jun 22, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_007129.5:c.1213_1216delinsGCATGT MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_009060.2:p.Pro405fs	frameshift
NC_000013.11:g.99985083_99985086delinsGCATGT
NC_000013.10:g.100637337_100637340delinsGCATGT
NG_007085.3:g.8328_8331delinsGCATGT
LRG_1157:g.8328_8331delinsGCATGT
LRG_1157t1:c.1213_1216delinsGCATGT	LRG_1157p1:p.Pro405fs

... more HGVS ... less HGVS

Protein change

P405fs

Other names

Canonical SPDI

NC_000013.11:99985082:CCCA:GCATGT

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help 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 Help 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.
ZIC2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	343	487

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help 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 Help 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.
Holoprosencephaly 5	Likely pathogenic (3)	criteria provided, multiple submitters, no conflicts	Jun 22, 2022	RCV002291071.4

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.
Likely pathogenic (Jun 22, 2022)	criteria provided, single submitter (('ACMG Guidelines, 2015) Method: research	Holoprosencephaly 5 Affected status: yes Allele origin: unknown	Wangler Lab, Baylor College of Medicine Accession: SCV002581935.1 First in ClinVar: Oct 15, 2022 Last updated: Oct 15, 2022	Publications: PubMed (1) PubMed: 11285244 Comment: This indel at c.1213_1216delinsGCATGT (p.Pro405Alafs9) was seen on exome through the Texome Project (R01HG011795). It has not been observed in healthy populations (PM2). This stop-gain … (more) This indel at c.1213_1216delinsGCATGT (p.Pro405Alafs9) was seen on exome through the Texome Project (R01HG011795). It has not been observed in healthy populations (PM2). This stop-gain variant is located in exon 2 of 3 and is predicted to be deleterious (PP3) and results in nonsense mediated decay in a gene where LOF is a documented mechanism of disease (PVS1) (PMID: 11285244). We determine this change to be likely pathogenic. (less) Clinical Features: Lobar holoprosencephaly (present) , Fused cervical vertebrae (present) , Global developmental delay (present) , Hearing impairment (present) , Gait disturbance (present) , Ankle weakness (present) … (more) Lobar holoprosencephaly (present) , Fused cervical vertebrae (present) , Global developmental delay (present) , Hearing impairment (present) , Gait disturbance (present) , Ankle weakness (present) , Delusion (present) , Atypical behavior (present) , Anxiety (present) , Migraine (present) , Chiari type I malformation (present) , Orbital cyst (present) (less) Sex: male Ethnicity/Population group: Hispanic Testing laboratory: Org:1006
Likely pathogenic (Jun 15, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Holoprosencephaly 5 Affected status: unknown Allele origin: unknown	Baylor Genetics Accession: SCV003835198.1 First in ClinVar: Mar 11, 2023 Last updated: Mar 11, 2023
not provided (-)	no classification provided Method: phenotyping only	Holoprosencephaly 5 Affected status: yes Allele origin: unknown	GenomeConnect - Brain Gene Registry Accession: SCV003931251.1 First in ClinVar: Jun 17, 2023 Last updated: Jun 17, 2023	Comment: Variant classified as Likely pathogenic and reported on 06-15-2022 by Baylor Medical Genetics Laboratories. Assertions are reported exactly as they appear on the patient provided … (more) Variant classified as Likely pathogenic and reported on 06-15-2022 by Baylor Medical Genetics Laboratories. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/. (less) Clinical Features: Intellectual disability (present) , Lobar holoprosencephaly (present) , Fused cervical vertebrae (present) , Global developmental delay (present) , Hearing impairment (present) , Gait disturbance (present) … (more) Intellectual disability (present) , Lobar holoprosencephaly (present) , Fused cervical vertebrae (present) , Global developmental delay (present) , Hearing impairment (present) , Gait disturbance (present) , Ankle weakness (present) , Delusion (present) , Atypical behavior (present) , Anxiety (present) , Chiari type I malformation (present) , Migraine (present) , Orbital cyst (present) (less) Indication for testing: Diagnostic Age: 40-49 years Sex: male Method: Exome Sequencing Testing laboratory: Baylor Genetics Date variant was reported to submitter: 2022-06-15 Testing laboratory interpretation: Likely pathogenic

Comment:

This indel at c.1213_1216delinsGCATGT (p.Pro405Alafs*9) was seen on exome through the Texome Project (R01HG011795). It has not been observed in healthy populations (PM2). This stop-gain variant is located in exon 2 of 3 and is predicted to be deleterious (PP3) and results in nonsense mediated decay in a gene where LOF is a documented mechanism of disease (PVS1) (PMID: 11285244). We determine this change to be likely pathogenic.

Comment:

Variant classified as Likely pathogenic and reported on 06-15-2022 by Baylor Medical Genetics Laboratories. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.

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.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Holoprosencephaly due to mutations in ZIC2: alanine tract expansion mutations may be caused by parental somatic recombination.	Brown LY	Human molecular genetics	2001	PMID: 11285244

Text-mined citations for this variant ...

Record last updated Jun 23, 2024

ClinVar Genomic variation as it relates to human health

NM_007129.5(ZIC2):c.1213_1216delinsGCATGT (p.Pro405fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...