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NM_000429.3(MAT1A):c.763C>T (p.Pro255Ser) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 5, 2017
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:
RCV000433867.2

Allele description [Variation Report for NM_000429.3(MAT1A):c.763C>T (p.Pro255Ser)]

NM_000429.3(MAT1A):c.763C>T (p.Pro255Ser)

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.763C>T (p.Pro255Ser)
HGVS:
  • NC_000010.11:g.80276381G>A
  • NG_008083.1:g.18298C>T
  • NM_000429.3:c.763C>TMANE SELECT
  • NP_000420.1:p.Pro255Ser
  • NC_000010.10:g.82036137G>A
  • NM_000429.2:c.763C>T
Protein change:
P255S
Links:
dbSNP: rs913435613
NCBI 1000 Genomes Browser:
rs913435613
Molecular consequence:
  • NM_000429.3:c.763C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000513537GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Oct 5, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000513537.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The P255S variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The P255S variant is not observed in large population cohorts (Lek et al., 2016). The P255S variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. Furthermore, P255 is located in a region of the MAT1A protein (F250-A259) that is highly conserved and is believed to be involved in methionine positioning in the active site (, and multiple missense variants in nearby residues (I252T, G257R, D258G, A259V) have been reported in the Human Gene Mutation Database in association with methionine adenosyltransferase I/III (MAT I/III) deficiency (Stenson et al., 2014), supporting the functional importance of this region of the protein. In summary, we interpret this variant as likely pathogenic.

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

Last Updated: Sep 29, 2024