NM_005984.5(SLC25A1):c.844C>T (p.Arg282Cys) AND 2-hydroxyglutaric aciduria

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Nov 12, 2020
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000035018.36

Allele description [Variation Report for NM_005984.5(SLC25A1):c.844C>T (p.Arg282Cys)]

NM_005984.5(SLC25A1):c.844C>T (p.Arg282Cys)

Gene:

SLC25A1:solute carrier family 25 member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_005984.5(SLC25A1):c.844C>T (p.Arg282Cys)

HGVS:

NC_000022.11:g.19176222G>A
NG_033863.1:g.7642C>T
NM_001256534.2:c.865C>T
NM_001287387.2:c.535C>T
NM_005984.5:c.844C>TMANE SELECT
NP_001243463.1:p.Arg289Cys
NP_001274316.1:p.Arg179Cys
NP_005975.1:p.Arg282Cys
NP_005975.1:p.Arg282Cys
NP_005975.1:p.Arg282Cys
NC_000022.10:g.19163735G>A
NM_005984.3:c.844C>T
NM_005984.4:c.844C>T
NR_046298.3:n.768C>T
P53007:p.Arg282Cys

Protein change:

R179C; ARG282CYS

Links:

UniProtKB: P53007#VAR_069495; OMIM: 190315.0002; dbSNP: rs431905509

NCBI 1000 Genomes Browser:

rs431905509

Molecular consequence:

NM_001256534.2:c.865C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001287387.2:c.535C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_005984.5:c.844C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_046298.3:n.768C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: 2-hydroxyglutaric aciduria (D2L2AD)
Identifiers:: MONDO: MONDO:0016001; MedGen: C2746066; Orphanet: 356978

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000992582	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-SouthSeq	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jul 23, 2019)	maternal	research	PubMed (1) [See all records that cite this PMID]
SCV001934316	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 12, 2020)	paternal	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

SCV000992582

HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-SouthSeq

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jul 23, 2019)

maternal

research

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

SCV001934316

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 12, 2020)

paternal

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	maternal	yes	1	not provided	not provided	1	not provided	research
not provided	paternal	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-SouthSeq, SCV000992582.2

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

Description

ACMG codes: PS3, PM2, PM3, PP3

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

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001934316.1

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

Description

This variant was identified as compound heterozygous with NM_005984.5:c.578C>T.

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

Last Updated: Nov 10, 2024

ClinVar

Relating variation to medicine