NM_001111.5(ADAR):c.2624A>G (p.Lys875Arg) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 6, 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:: RCV002853101.3

Allele description [Variation Report for NM_001111.5(ADAR):c.2624A>G (p.Lys875Arg)]

NM_001111.5(ADAR):c.2624A>G (p.Lys875Arg)

Genes:

LOC126805874:CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:154561176-154562375 [Gene]
ADAR:adenosine deaminase RNA specific [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q21.3

Genomic location:

Preferred name:

NM_001111.5(ADAR):c.2624A>G (p.Lys875Arg)

HGVS:

NC_000001.11:g.154589801T>C
NG_011844.2:g.46760A>G
NG_082198.1:g.1202T>C
NM_001025107.3:c.1739A>G
NM_001111.5:c.2624A>GMANE SELECT
NM_001193495.2:c.1739A>G
NM_001365045.1:c.2651A>G
NM_001365046.1:c.1739A>G
NM_001365047.1:c.1739A>G
NM_001365048.1:c.1739A>G
NM_001365049.1:c.1661A>G
NM_015840.4:c.2546A>G
NM_015841.4:c.2489A>G
NP_001020278.1:p.Lys580Arg
NP_001102.3:p.Lys875Arg
NP_001180424.1:p.Lys580Arg
NP_001351974.1:p.Lys884Arg
NP_001351975.1:p.Lys580Arg
NP_001351976.1:p.Lys580Arg
NP_001351977.1:p.Lys580Arg
NP_001351978.1:p.Lys554Arg
NP_056655.3:p.Lys849Arg
NP_056656.3:p.Lys830Arg
LRG_1212t1:c.2624A>G
LRG_1212:g.46760A>G
LRG_1212p1:p.Lys875Arg
NC_000001.10:g.154562277T>C

Protein change:

K554R

Molecular consequence:

NM_001025107.3:c.1739A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001111.5:c.2624A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001193495.2:c.1739A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365045.1:c.2651A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365046.1:c.1739A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365047.1:c.1739A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365048.1:c.1739A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001365049.1:c.1661A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015840.4:c.2546A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015841.4:c.2489A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Symmetrical dyschromatosis of extremities (DSH)
Synonyms:: Dyschromatosis symmetrica hereditaria 1; Dyschromatosis symmetrica hereditaria; Familial reticulate acropigmentation of Dohi; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007483; MedGen: C0406775; Orphanet: 41; OMIM: 127400

Name:: Aicardi-Goutieres syndrome 6 (AGS6)
Identifiers:: MONDO: MONDO:0014007; MedGen: C3539013; Orphanet: 51; OMIM: 615010

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LOC126862205 [Homo sapiens]
LOC126862205 [Homo sapiens]
Gene ID:126862205

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003226088	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 6, 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

SCV003226088

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 6, 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, SCV003226088.2

#	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 lysine, which is basic and polar, with arginine, which is basic and polar, at codon 875 of the ADAR protein (p.Lys875Arg). This variant is present in population databases (rs751955732, gnomAD 0.008%). 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 (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with ADAR-related conditions.

#	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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