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NM_001077365.2(POMT1):c.141T>G (p.Tyr47Ter) AND Inborn genetic diseases

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 8, 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:
RCV002707991.2

Allele description [Variation Report for NM_001077365.2(POMT1):c.141T>G (p.Tyr47Ter)]

NM_001077365.2(POMT1):c.141T>G (p.Tyr47Ter)

Gene:
POMT1:protein O-mannosyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.13
Genomic location:
Preferred name:
NM_001077365.2(POMT1):c.141T>G (p.Tyr47Ter)
HGVS:
  • NC_000009.12:g.131506132T>G
  • NG_008896.2:g.8231T>G
  • NM_001077365.2:c.141T>GMANE SELECT
  • NM_001077366.2:c.-22T>G
  • NM_001136113.2:c.141T>G
  • NM_001136114.2:c.-122-271T>G
  • NM_001353193.2:c.141T>G
  • NM_001353194.2:c.-22T>G
  • NM_001353195.2:c.-122-271T>G
  • NM_001353196.2:c.123-271T>G
  • NM_001353197.2:c.-22T>G
  • NM_001353198.2:c.-22T>G
  • NM_001353199.2:c.-122-271T>G
  • NM_001353200.2:c.-80-271T>G
  • NM_001374689.1:c.-22T>G
  • NM_001374690.1:c.141T>G
  • NM_001374691.1:c.-71-1236T>G
  • NM_001374692.1:c.-71-1236T>G
  • NM_001374693.1:c.-22T>G
  • NM_001374695.1:c.-30+1792T>G
  • NM_007171.4:c.141T>G
  • NP_001070833.1:p.Tyr47Ter
  • NP_001129585.1:p.Tyr47Ter
  • NP_001340122.2:p.Tyr47Ter
  • NP_001361619.1:p.Tyr47Ter
  • NP_009102.4:p.Tyr47Ter
  • LRG_842t1:c.141T>G
  • LRG_842t2:c.141T>G
  • LRG_842:g.8231T>G
  • LRG_842p1:p.Tyr47Ter
  • LRG_842p2:p.Tyr47Ter
  • NC_000009.11:g.134381519T>G
  • NM_007171.3:c.141T>G
  • NR_148391.2:n.175T>G
  • NR_148392.2:n.327T>G
  • NR_148393.2:n.175T>G
  • NR_148394.2:n.175T>G
  • NR_148395.2:n.327T>G
  • NR_148398.2:n.175T>G
  • NR_148399.2:n.567T>G
Protein change:
Y47*
Molecular consequence:
  • NM_001077366.2:c.-22T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353194.2:c.-22T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353197.2:c.-22T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353198.2:c.-22T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374689.1:c.-22T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374693.1:c.-22T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001136114.2:c.-122-271T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353195.2:c.-122-271T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353196.2:c.123-271T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353199.2:c.-122-271T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353200.2:c.-80-271T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374691.1:c.-71-1236T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374692.1:c.-71-1236T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374695.1:c.-30+1792T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NR_148391.2:n.175T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.327T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.175T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.175T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.327T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.175T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.567T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001077365.2:c.141T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001136113.2:c.141T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353193.2:c.141T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374690.1:c.141T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_007171.4:c.141T>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003556183Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Jun 8, 2021) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.

Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, et al.

Science. 2015 May 8;348(6235):666-9. doi: 10.1126/science.1261877.

PubMed [citation]
PMID:
25954003
PMCID:
PMC4537935

The rules and impact of nonsense-mediated mRNA decay in human cancers.

Lindeboom RG, Supek F, Lehner B.

Nat Genet. 2016 Oct;48(10):1112-8. doi: 10.1038/ng.3664. Epub 2016 Sep 12.

PubMed [citation]
PMID:
27618451
PMCID:
PMC5045715
See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV003556183.2

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

Description

The c.141T>G (p.Y47*) alteration, located in exon 3 (coding exon 2) of the POMT1 gene, consists of a T to G substitution at nucleotide position 141. This changes the amino acid from a tyrosine (Y) to a stop codon at amino acid position 47. The predicted stop codon occurs in the 5' end of the POMT1 gene. Premature termination codons in the 5’ end of a gene have been reported to escape nonsense-mediated mRNA decay and/or lead to re-initiation (Rivas, 2015; Lindeboom, 2016; Rhee, 2017). Direct evidence for this alteration is unavailable, however premature termination codons are typically deleterious in nature. Based on data from the Genome Aggregation Database (gnomAD), the POMT1 c.141T>G alteration was not observed, with coverage at this position. Based on the available evidence, this alteration is classified as likely pathogenic.

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

Last Updated: May 1, 2024