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NM_015378.4(VPS13D):c.12140A>G (p.Asn4047Ser) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Jun 1, 2023
Review status:
criteria provided, conflicting classifications
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002014268.13

Allele description [Variation Report for NM_015378.4(VPS13D):c.12140A>G (p.Asn4047Ser)]

NM_015378.4(VPS13D):c.12140A>G (p.Asn4047Ser)

Gene:
VPS13D:vacuolar protein sorting 13 homolog D [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.22
Genomic location:
Preferred name:
NM_015378.4(VPS13D):c.12140A>G (p.Asn4047Ser)
HGVS:
  • NC_000001.11:g.12415196A>G
  • NG_056877.1:g.190158A>G
  • NM_015378.4:c.12140A>GMANE SELECT
  • NM_018156.4:c.12065A>G
  • NP_056193.2:p.Asn4047Ser
  • NP_060626.2:p.Asn4022Ser
  • LRG_1213t1:c.12140A>G
  • LRG_1213:g.190158A>G
  • LRG_1213p1:p.Asn4047Ser
  • NC_000001.10:g.12475249A>G
Protein change:
N4022S
Links:
dbSNP: rs138906978
NCBI 1000 Genomes Browser:
rs138906978
Molecular consequence:
  • NM_015378.4:c.12140A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_018156.4:c.12065A>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002305561Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jul 19, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004009737CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely benign
(Jun 1, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV002305561.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 4047 of the VPS13D protein (p.Asn4047Ser). This variant is present in population databases (rs138906978, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with VPS13D-related conditions. ClinVar contains an entry for this variant (Variation ID: 1510978). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV004009737.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

VPS13D: BS1

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 17, 2024