VCV000692324.19 - ClinVar

NM_015378.4(VPS13D):c.4243G>A (p.Asp1415Asn)

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.

(4)

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.

Conflicting classifications of pathogenicity
Uncertain significance(1); Benign(2)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_015378.4(VPS13D):c.4243G>A (p.Asp1415Asn)

Variation ID: 692324 Accession: VCV000692324.19

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 1p36.22 1: 12277831 (GRCh38) [ NCBI UCSC ] 1: 12337888 (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 8, 2019	Oct 20, 2024	Jan 19, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_015378.4:c.4243G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_056193.2:p.Asp1415Asn	missense
NM_015378.3:c.4243G>A
NM_018156.4:c.4243G>A	NP_060626.2:p.Asp1415Asn	missense
NC_000001.11:g.12277831G>A
NC_000001.10:g.12337888G>A
NG_056877.1:g.52793G>A
LRG_1213:g.52793G>A
LRG_1213t1:c.4243G>A	LRG_1213p1:p.Asp1415Asn

... more HGVS ... less HGVS

Protein change

D1415N

Other names

Canonical SPDI

NC_000001.11:12277830: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.

0.00260 (A)

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

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054

The Genome Aggregation Database (gnomAD) 0.00112

Trans-Omics for Precision Medicine (TOPMed) 0.00167

1000 Genomes Project 30x 0.00234

1000 Genomes Project 0.00260

Exome Aggregation Consortium (ExAC) 0.00272

The Genome Aggregation Database (gnomAD), exomes 0.00280

Links

dbSNP: rs79282181 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.
VPS13D		-	-	GRCh38 GRCh37	1260	1312

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.
Arthrogryposis multiplex congenita Fetal akinesia deformation sequence 1	Uncertain significance (1)	criteria provided, single submitter	Jun 28, 2019	RCV000855522.2
not provided	Benign (2)	criteria provided, multiple submitters, no conflicts	Jan 19, 2024	RCV002064422.17
VPS13D-related disorder	Benign (1)	no assertion criteria provided	Jun 12, 2019	RCV003908141.2

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.
Uncertain significance (Jun 28, 2019)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: research	Arthrogryposis multiplex congenita Fetal akinesia sequence Affected status: yes Allele origin: maternal	Cirak Lab, University Hospital Cologne Accession: SCV000996652.1 First in ClinVar: Nov 08, 2019 Last updated: Nov 08, 2019	Publications: PubMed (1) PubMed: 31680123 Number of individuals with the variant: 1 Sex: female Ethnicity/Population group: German-Chinese Geographic origin: Germany
Benign (Jan 19, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV002464968.3 First in ClinVar: Apr 08, 2022 Last updated: Feb 14, 2024
Benign (Feb 01, 2023)	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV003916057.13 First in ClinVar: Apr 23, 2023 Last updated: Oct 20, 2024	Comment: VPS13D: BS1, BS2 Number of individuals with the variant: 1
Benign (Jun 12, 2019)	no assertion criteria provided Method: clinical testing	VPS13D-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004719898.2 First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024	Comment: This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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
The genomic and clinical landscape of fetal akinesia.	Pergande M	Genetics in medicine : official journal of the American College of Medical Genetics	2020	PMID: 31680123

Text-mined citations for rs79282181 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 20, 2024

ClinVar Genomic variation as it relates to human health

NM_015378.4(VPS13D):c.4243G>A (p.Asp1415Asn)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs79282181 ...