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NM_000429.3(MAT1A):c.812A>G (p.Tyr271Cys) AND Hepatic methionine adenosyltransferase deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 7, 2021
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:
RCV001882238.6

Allele description [Variation Report for NM_000429.3(MAT1A):c.812A>G (p.Tyr271Cys)]

NM_000429.3(MAT1A):c.812A>G (p.Tyr271Cys)

Gene:
MAT1A:methionine adenosyltransferase 1A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q22.3
Genomic location:
Preferred name:
NM_000429.3(MAT1A):c.812A>G (p.Tyr271Cys)
HGVS:
  • NC_000010.11:g.80275156T>C
  • NG_008083.1:g.19523A>G
  • NM_000429.3:c.812A>GMANE SELECT
  • NP_000420.1:p.Tyr271Cys
  • NC_000010.10:g.82034912T>C
Protein change:
Y271C
Links:
dbSNP: rs1841469345
NCBI 1000 Genomes Browser:
rs1841469345
Molecular consequence:
  • NM_000429.3:c.812A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hepatic methionine adenosyltransferase deficiency
Synonyms:
MAT I/III DEFICIENCY; Isolated Persistent Hypermethioninemia; Methionine adenosyltransferase deficiency; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009607; MeSH: C564683; MedGen: C0268621; Orphanet: 168598; OMIM: 250850

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002162698Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 7, 2021) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Neonatal methionine adenosyltransferase I/III deficiency with abnormal signal intensity in the central tegmental tract.

Kido J, Sawada T, Momosaki K, Suzuki Y, Uetani H, Kitajima M, Mitsubuchi H, Nakamura K, Matsumoto S.

Brain Dev. 2019 Apr;41(4):382-388. doi: 10.1016/j.braindev.2018.10.010. Epub 2018 Oct 30.

PubMed [citation]
PMID:
30389272

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, SCV002162698.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

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 disruptive. This variant has been observed in individuals with autosomal recessive hypermethioninemia (PMID: 30389272; Invitae). This variant is not present in population databases (ExAC no frequency). This sequence change replaces tyrosine with cysteine at codon 271 of the MAT1A protein (p.Tyr271Cys). The tyrosine residue is highly conserved and there is a large physicochemical difference between tyrosine and cysteine.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024