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NM_001048174.2(MUTYH):c.1393-1G>A AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 18, 2020
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:
RCV002392934.2

Allele description [Variation Report for NM_001048174.2(MUTYH):c.1393-1G>A]

NM_001048174.2(MUTYH):c.1393-1G>A

Gene:
MUTYH:mutY DNA glycosylase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p34.1
Genomic location:
Preferred name:
NM_001048174.2(MUTYH):c.1393-1G>A
HGVS:
  • NC_000001.11:g.45330558C>T
  • NG_008189.1:g.14913G>A
  • NM_001048171.2:c.1393-1G>A
  • NM_001048172.2:c.1396-1G>A
  • NM_001048173.2:c.1393-1G>A
  • NM_001048174.2:c.1393-1G>AMANE SELECT
  • NM_001128425.2:c.1477-1G>A
  • NM_001293190.2:c.1438-1G>A
  • NM_001293191.2:c.1426-1G>A
  • NM_001293192.2:c.1117-1G>A
  • NM_001293195.2:c.1393-1G>A
  • NM_001293196.2:c.1117-1G>A
  • NM_001350650.2:c.1048-1G>A
  • NM_001350651.2:c.1048-1G>A
  • NM_001407069.1:c.1426-1G>A
  • NM_001407070.1:c.1393-1G>A
  • NM_001407071.1:c.1396-1G>A
  • NM_001407072.1:c.1393-1G>A
  • NM_001407073.1:c.1393-1G>A
  • NM_001407075.1:c.1309-1G>A
  • NM_001407077.1:c.1426-1G>A
  • NM_001407078.1:c.1396-1G>A
  • NM_001407079.1:c.1354-1G>A
  • NM_001407080.1:c.1351-1G>A
  • NM_001407081.1:c.1393-1G>A
  • NM_001407082.1:c.1048-1G>A
  • NM_001407083.1:c.1435-1G>A
  • NM_001407085.1:c.1435-1G>A
  • NM_001407086.1:c.1396-1G>A
  • NM_001407087.1:c.1414-1G>A
  • NM_001407088.1:c.1393-1G>A
  • NM_001407089.1:c.1393-1G>A
  • NM_001407091.1:c.1117-1G>A
  • NM_012222.3:c.1468-1G>A
  • LRG_220t1:c.1477-1G>A
  • LRG_220:g.14913G>A
  • NC_000001.10:g.45796230C>T
  • NM_001048171.1:c.1435-1G>A
  • NM_001128425.1:c.1477-1G>A
Links:
dbSNP: rs1057517459
NCBI 1000 Genomes Browser:
rs1057517459
Molecular consequence:
  • NM_001048171.2:c.1393-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001048172.2:c.1396-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001048173.2:c.1393-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001048174.2:c.1393-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001128425.2:c.1477-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001293190.2:c.1438-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001293191.2:c.1426-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001293192.2:c.1117-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001293195.2:c.1393-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001293196.2:c.1117-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001350650.2:c.1048-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001350651.2:c.1048-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407069.1:c.1426-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407070.1:c.1393-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407071.1:c.1396-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407072.1:c.1393-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407073.1:c.1393-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407075.1:c.1309-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407077.1:c.1426-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407078.1:c.1396-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407079.1:c.1354-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407080.1:c.1351-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407081.1:c.1393-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407082.1:c.1048-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407083.1:c.1435-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407085.1:c.1435-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407086.1:c.1396-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407087.1:c.1414-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407088.1:c.1393-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407089.1:c.1393-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001407091.1:c.1117-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_012222.3:c.1468-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Hereditary neoplastic syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002697063Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Sep 18, 2020) 		germlineclinical testing

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

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase.

Wang L, Lee SJ, Verdine GL.

J Biol Chem. 2015 Jul 10;290(28):17096-105. doi: 10.1074/jbc.M115.657866. Epub 2015 May 20.

PubMed [citation]
PMID:
25995449
PMCID:
PMC4498048

Details of each submission

From Ambry Genetics, SCV002697063.2

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

Description

The c.1477-1G>A intronic variant results from a G to A substitution one nucleotide upstream from coding exon 15 of the MUTYH gene. Alterations that disrupt the canonical splice site are expected to result in aberrant splicing. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNA decay; however, direct evidence is unavailable. The exact functional effect of the missing amino acids at the 3' terminus of the MUTYH gene, which impacts the last 14 AA of the protein, is unknown; however, the impacted region is critical for protein function (Ambry internal data; Wang L et al. J. Biol. Chem., 2015 Jul;290:17096-105). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

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

Last Updated: May 16, 2025