NM_012463.4(ATP6V0A2):c.1357A>G (p.Ile453Val) AND ALG9 congenital disorder of glycosylation

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 25, 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:: RCV002544083.3

Allele description [Variation Report for NM_012463.4(ATP6V0A2):c.1357A>G (p.Ile453Val)]

NM_012463.4(ATP6V0A2):c.1357A>G (p.Ile453Val)

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.1357A>G (p.Ile453Val)

HGVS:

NC_000012.12:g.123744627A>G
NG_012743.1:g.37310A>G
NM_012463.4:c.1357A>GMANE SELECT
NP_036595.2:p.Ile453Val
NC_000012.11:g.124229174A>G
NM_012463.3:c.1357A>G

Protein change:

I453V

Links:

dbSNP: rs911881776

NCBI 1000 Genomes Browser:

rs911881776

Molecular consequence:

NM_012463.4:c.1357A>G - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002938234	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 25, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002938234

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 25, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV002938234.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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 output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 1310504). This variant has not been reported in the literature in individuals affected with ATP6V0A2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 453 of the ATP6V0A2 protein (p.Ile453Val).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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