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NM_000429.3(MAT1A):c.406-3C>T AND Hepatic methionine adenosyltransferase deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 22, 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:
RCV001963660.4

Allele description [Variation Report for NM_000429.3(MAT1A):c.406-3C>T]

NM_000429.3(MAT1A):c.406-3C>T

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.406-3C>T
HGVS:
  • NC_000010.11:g.80280319G>A
  • NG_008083.1:g.14360C>T
  • NM_000429.3:c.406-3C>TMANE SELECT
  • NC_000010.10:g.82040075G>A
Links:
dbSNP: rs374316399
NCBI 1000 Genomes Browser:
rs374316399
Molecular consequence:
  • NM_000429.3:c.406-3C>T - intron variant - [Sequence Ontology: SO:0001627]

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
SCV002249416Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 22, 2022) 		germlineclinical testing

PubMed (3)
[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

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002249416.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. This variant has not been reported in the literature in individuals affected with MAT1A-related conditions. This variant is present in population databases (rs374316399, gnomAD 0.0009%). This sequence change falls in intron 4 of the MAT1A gene. It does not directly change the encoded amino acid sequence of the MAT1A protein. It affects a nucleotide within the consensus splice site.

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

Last Updated: Sep 29, 2024