NM_006015.6(ARID1A):c.364G>C (p.Gly122Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 28, 2023
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:: RCV003575429.2

Allele description [Variation Report for NM_006015.6(ARID1A):c.364G>C (p.Gly122Arg)]

NM_006015.6(ARID1A):c.364G>C (p.Gly122Arg)

Gene:

ARID1A:AT-rich interaction domain 1A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.11

Genomic location:

Preferred name:

NM_006015.6(ARID1A):c.364G>C (p.Gly122Arg)

HGVS:

NC_000001.11:g.26696767G>C
NG_029965.1:g.5737G>C
NG_090122.2:g.2020G>C
NM_006015.6:c.364G>CMANE SELECT
NM_139135.4:c.364G>C
NP_006006.3:p.Gly122Arg
NP_006006.3:p.Gly122Arg
NP_624361.1:p.Gly122Arg
LRG_875t1:c.364G>C
LRG_875:g.5737G>C
LRG_875p1:p.Gly122Arg
NC_000001.10:g.27023258G>C
NM_006015.4:c.364G>C

Protein change:

G122R

Molecular consequence:

NM_006015.6:c.364G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_139135.4:c.364G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha, isoform CRA_...
protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha, isoform CRA_c, partial [Homo sapiens]
gi|119599530|gb|EAW79124.1||gnl|WGS |hCP1785782

Protein
Protopterus dolloi (African lungfish) nasal lymphoid aggregates
Protopterus dolloi (African lungfish) nasal lymphoid aggregates

biosample
Chain A, Proline iminopeptidase
Chain A, Proline iminopeptidase
gi|73535541|pdb|1XRO|A

Protein
Protein Family Models for Protein (Select 1221766090) (11)
Protein Family Models
Millettieae 18S ribosomal RNA gene, partial sequence; internal transcribed space...
Millettieae 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence.
PopSet: 734691181

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004364549	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 28, 2023)	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

SCV004364549

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 28, 2023)

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, SCV004364549.1

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

Description

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 122 of the ARID1A protein (p.Gly122Arg). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ARID1A-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ARID1A protein function with a negative predictive value of 95%. 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: Sep 29, 2024

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