NM_012463.4(ATP6V0A2):c.63G>T (p.Thr21=) AND ALG9 congenital disorder of glycosylation

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jul 23, 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:: RCV002632836.3

Allele description [Variation Report for NM_012463.4(ATP6V0A2):c.63G>T (p.Thr21=)]

NM_012463.4(ATP6V0A2):c.63G>T (p.Thr21=)

Genes:

LOC130009117:ATAC-STARR-seq lymphoblastoid silent region 5049 [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.63G>T (p.Thr21=)

HGVS:

NC_000012.12:g.123712628G>T
NG_012743.1:g.5311G>T
NM_012463.4:c.63G>TMANE SELECT
NP_036595.2:p.Thr21=
NP_036595.2:p.Thr21=
NC_000012.11:g.124197175G>T
NM_012463.2:c.63G>T

Molecular consequence:

NM_012463.4:c.63G>T - synonymous variant - [Sequence Ontology: SO:0001819]

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

Recent activity

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PREDICTED: Rattus norvegicus ADAM metallopeptidase domain 18 (Adam18), transcrip...
PREDICTED: Rattus norvegicus ADAM metallopeptidase domain 18 (Adam18), transcript variant X11, mRNA
gi|2678903983|ref|XM_063275670.1|

Nucleotide
Agrocybe cylindracea culture CBS:205.46 strain CBS 205.46 small subunit ribosoma...
Agrocybe cylindracea culture CBS:205.46 strain CBS 205.46 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
gi|1473243220|gb|MH856164.1|

Nucleotide
MIGS Eukaryotic sample from Pholiota microspora
MIGS Eukaryotic sample from Pholiota microspora

biosample
RHTO_08170 [Rhodotorula toruloides NP11]
RHTO_08170 [Rhodotorula toruloides NP11]
Gene ID:27372183

Gene
Formocresols
Formocresols
Compounds consisting of formaldehyde, cresol, GLYCERIN, and water. They are used in the PULPOTOMY of PRIMARY TEETH and as ROOT CANAL IRRIGANTS.<br/>Year introduced: 1973(1972)

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003510369	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jul 23, 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

SCV003510369

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jul 23, 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, SCV003510369.2

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

#	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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