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NM_006412.4(AGPAT2):c.475C>T (p.Arg159Cys) AND Monogenic diabetes

Germline classification:
Benign (1 submission)
Last evaluated:
Feb 22, 2019
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:
RCV000445508.5

Allele description [Variation Report for NM_006412.4(AGPAT2):c.475C>T (p.Arg159Cys)]

NM_006412.4(AGPAT2):c.475C>T (p.Arg159Cys)

Gene:
AGPAT2:1-acylglycerol-3-phosphate O-acyltransferase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.3
Genomic location:
Preferred name:
NM_006412.4(AGPAT2):c.475C>T (p.Arg159Cys)
Other names:
p.Arg159Cys
HGVS:
  • NC_000009.12:g.136676978G>A
  • NG_008090.1:g.15482C>T
  • NM_001012727.2:c.475C>T
  • NM_006412.4:c.475C>TMANE SELECT
  • NP_001012745.1:p.Arg159Cys
  • NP_006403.2:p.Arg159Cys
  • NC_000009.11:g.139571430G>A
  • NM_006412.3:c.475C>T
Protein change:
R159C
Links:
dbSNP: rs142993240
NCBI 1000 Genomes Browser:
rs142993240
Molecular consequence:
  • NM_001012727.2:c.475C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006412.4:c.475C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Monogenic diabetes
Identifiers:
MONDO: MONDO:0015967; MedGen: C3888631

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000537070Personalized Diabetes Medicine Program, University of Maryland School of Medicine
criteria provided, single submitter

(ACMG Guidelines, 2015)		Benign
(Feb 22, 2019) 		unknownresearch

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknown5not providednot providednot providednot providedresearch

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 Personalized Diabetes Medicine Program, University of Maryland School of Medicine, SCV000537070.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided5not providednot providedresearch PubMed (1)

Description

ACMG criteria: BS1 (1% in gnomAD AJ population, 0.5% overall MAF in gnomAD; disease prevalence 1:10 million gives MAF of 0.03%), BS2 (8 homozygotes in gnomAD) [REVEL 0.582, BP4 (3 predictors), PP3 (6 predictors)= conflicting evidence, not using]; heterozygotes mutation found in brother and sister with lipodytrophy phenotype Simsir et al. 2015 ""Heterozygous AGPAT2 Mutation, Diabetes, and Lipodystrophy in Extremities"" (no PMID)= benign

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot provided5not providednot providednot provided

Last Updated: Jul 13, 2025