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NM_012463.4(ATP6V0A2):c.1309C>A (p.Leu437Ile) AND ALG9 congenital disorder of glycosylation

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 14, 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:
RCV002302058.4

Allele description [Variation Report for NM_012463.4(ATP6V0A2):c.1309C>A (p.Leu437Ile)]

NM_012463.4(ATP6V0A2):c.1309C>A (p.Leu437Ile)

Gene:
ATP6V0A2:ATPase H+ transporting V0 subunit a2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q24.31
Genomic location:
Preferred name:
NM_012463.4(ATP6V0A2):c.1309C>A (p.Leu437Ile)
HGVS:
  • NC_000012.12:g.123744320C>A
  • NG_012743.1:g.37003C>A
  • NM_012463.4:c.1309C>AMANE SELECT
  • NP_036595.2:p.Leu437Ile
  • NP_036595.2:p.Leu437Ile
  • NC_000012.11:g.124228867C>A
  • NM_012463.2:c.1309C>A
Protein change:
L437I
Molecular consequence:
  • NM_012463.4:c.1309C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
ALG9 congenital disorder of glycosylation (CDG1L)
Synonyms:
CDG Il; CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Il; CDG 1L; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012117; MedGen: C2931006; Orphanet: 79328; OMIM: 608776

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002597925Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 14, 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, SCV002597925.3

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

Description

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"). This variant has not been reported in the literature in individuals affected with ATP6V0A2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 437 of the ATP6V0A2 protein (p.Leu437Ile). 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

Last Updated: Sep 29, 2024