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NM_152415.3(VPS37A):c.31G>T (p.Ala11Ser) AND Hereditary spastic paraplegia 53

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 17, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002596561.3

Allele description [Variation Report for NM_152415.3(VPS37A):c.31G>T (p.Ala11Ser)]

NM_152415.3(VPS37A):c.31G>T (p.Ala11Ser)

Gene:
VPS37A:VPS37A subunit of ESCRT-I [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8p22
Genomic location:
Preferred name:
NM_152415.3(VPS37A):c.31G>T (p.Ala11Ser)
HGVS:
  • NC_000008.11:g.17247275G>T
  • NG_032996.2:g.5384G>T
  • NG_113547.1:g.770G>T
  • NM_001145152.2:c.31G>T
  • NM_001363167.1:c.31G>T
  • NM_001363168.1:c.-285G>T
  • NM_001363169.1:c.-235G>T
  • NM_001363170.1:c.-285G>T
  • NM_001363171.1:c.-235G>T
  • NM_001363172.2:c.-285G>T
  • NM_001363173.2:c.31G>T
  • NM_152415.3:c.31G>TMANE SELECT
  • NP_001138624.1:p.Ala11Ser
  • NP_001350096.1:p.Ala11Ser
  • NP_001350102.1:p.Ala11Ser
  • NP_689628.2:p.Ala11Ser
  • NC_000008.10:g.17104784G>T
Protein change:
A11S
Molecular consequence:
  • NM_001363168.1:c.-285G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001363169.1:c.-235G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001363170.1:c.-285G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001363171.1:c.-235G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001363172.2:c.-285G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001145152.2:c.31G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363167.1:c.31G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363173.2:c.31G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152415.3:c.31G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary spastic paraplegia 53
Synonyms:
Spastic paraplegia 53, autosomal recessive
Identifiers:
MONDO: MONDO:0013962; MedGen: C3539494; Orphanet: 319199; OMIM: 614898

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002941158Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 17, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002941158.2

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with VPS37A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 11 of the VPS37A protein (p.Ala11Ser).

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

Last Updated: Sep 29, 2024