VCV002628316.1 - ClinVar

NM_019059.5(TOMM7):c.86C>T (p.Pro29Leu)

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.

(1)

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.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_019059.5(TOMM7):c.86C>T (p.Pro29Leu)

Variation ID: 2628316 Accession: VCV002628316.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 7p15.3 7: 22822694 (GRCh38) [ NCBI UCSC ] 7: 22862313 (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	Nov 20, 2023	Nov 20, 2023	Nov 13, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_019059.5:c.86C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_061932.1:p.Pro29Leu	missense
NC_000007.14:g.22822694G>A
NC_000007.13:g.22862313G>A
NG_110588.1:g.465G>A

Protein change

P29L

Other names

TOMM7, PRO29LEU (rs778567973)

Canonical SPDI

NC_000007.14:22822693:G:A

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

OMIM: 607980.0001 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.
TOMM7		-	-	GRCh38 GRCh37	6	40

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.
Garg-Mishra progeroid syndrome	Pathogenic (1)	no assertion criteria provided	Nov 13, 2023	RCV003397172.1

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.
Pathogenic (Nov 13, 2023)	no assertion criteria provided Method: literature only	GARG-MISHRA PROGEROID SYNDROME Affected status: not provided Allele origin: germline	OMIM Accession: SCV004102634.1 First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023	Publications: PubMed (1) PubMed: 36282599 Comment on evidence: In a 21-year-old man of Chinese ancestry (MAD 5700.25) with Garg-Mishra progeroid syndrome (GMPGS; 620601), Garg et al. (2022) identified homozygosity for a c.86C-T transition … (more) In a 21-year-old man of Chinese ancestry (MAD 5700.25) with Garg-Mishra progeroid syndrome (GMPGS; 620601), Garg et al. (2022) identified homozygosity for a c.86C-T transition (c.86C-T, NM_019059.4) in exon 1 of the TOMM7 gene, resulting in a pro29-to-leu (P29L) substitution at a highly conserved residue within an alpha-helix in the kinked transmembrane segment. The mutation was present in heterozygosity in the proband's unaffected parents and 2 unaffected sibs. DNA was unavailable from a similarly affected older sister who died at age 10 years. Although the P29L mutant showed normal localization to the mitochondria, immunoprecipitation studies in transfected HEK293 cells revealed poor interaction between the mutant protein and the core TOMM complex proteins, TOMM40 (608061) and TOMM22 (607046), and those results were replicated in HeLa cells. In addition, patient fibroblasts showed elevated basal and maximal oxygen consumption rates, compared to control cell lines. Gene-set enrichment analysis of the proband's mitochondrial proteome indicated a higher abundance of proteins related to ATP production and proton transport, and reduced expression of proteins related to phospholipid metabolic pathways. (less)

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

Title	Author	Journal	Year	Link
Autosomal recessive progeroid syndrome due to homozygosity for a TOMM7 variant.	Garg A	The Journal of clinical investigation	2022	PMID: 36282599

Text-mined citations for this variant ...

Record last updated Jun 23, 2024

ClinVar Genomic variation as it relates to human health

NM_019059.5(TOMM7):c.86C>T (p.Pro29Leu)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...