NM_012463.4(ATP6V0A2):c.1351C>T (p.Arg451Trp) AND ALG9 congenital disorder of glycosylation

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 14, 2021
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:: RCV001975534.4

Allele description [Variation Report for NM_012463.4(ATP6V0A2):c.1351C>T (p.Arg451Trp)]

NM_012463.4(ATP6V0A2):c.1351C>T (p.Arg451Trp)

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.1351C>T (p.Arg451Trp)

HGVS:

NC_000012.12:g.123744621C>T
NG_012743.1:g.37304C>T
NM_012463.4:c.1351C>TMANE SELECT
NP_036595.2:p.Arg451Trp
NC_000012.11:g.124229168C>T

Protein change:

R451W

Links:

dbSNP: rs907470146

NCBI 1000 Genomes Browser:

rs907470146

Molecular consequence:

NM_012463.4:c.1351C>T - 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
SCV002253472	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 14, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23806237, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002253472

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 14, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Molecular diagnostic testing for congenital disorders of glycosylation (CDG): detection rate for single gene testing and next generation sequencing panel testing.

Jones MA, Rhodenizer D, da Silva C, Huff IJ, Keong L, Bean LJ, Coffee B, Collins C, Tanner AK, He M, Hegde MR.

Mol Genet Metab. 2013 Sep-Oct;110(1-2):78-85. doi: 10.1016/j.ymgme.2013.05.012. Epub 2013 May 28.

PubMed [citation]

PMID:: 23806237

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, SCV002253472.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces arginine with tryptophan at codon 451 of the ATP6V0A2 protein (p.Arg451Trp). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with cutis laxa (PMID: 23806237). 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 disruptive. 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.

#	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: Dec 24, 2023

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