NM_001077365.2(POMT1):c.1474C>T (p.Arg492Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: Aug 21, 2018)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000760355.2

Allele description [Variation Report for NM_001077365.2(POMT1):c.1474C>T (p.Arg492Ter)]

NM_001077365.2(POMT1):c.1474C>T (p.Arg492Ter)

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.1474C>T (p.Arg492Ter)
HGVS:
  • NC_000009.12:g.131518945C>T
  • NG_008896.1:g.21044C>T
  • NM_001077365.2:c.1474C>TMANE SELECT
  • NM_001077366.2:c.1312C>T
  • NM_001136113.2:c.1474C>T
  • NM_001136114.2:c.1123C>T
  • NM_001353193.2:c.1540C>T
  • NM_001353194.2:c.1312C>T
  • NM_001353195.2:c.1123C>T
  • NM_001353196.2:c.1384C>T
  • NM_001353197.2:c.1378C>T
  • NM_001353198.2:c.1378C>T
  • NM_001353199.2:c.1189C>T
  • NM_001353200.2:c.1018C>T
  • NM_001374689.1:c.1462C>T
  • NM_001374690.1:c.1365+408C>T
  • NM_001374691.1:c.1123C>T
  • NM_001374692.1:c.1123C>T
  • NM_001374693.1:c.1123C>T
  • NM_001374695.1:c.1084C>T
  • NM_007171.3:c.1540C>T
  • NM_007171.4:c.1540C>T
  • NP_001070833.1:p.Arg492Ter
  • NP_001070834.1:p.Arg438Ter
  • NP_001129585.1:p.Arg492Ter
  • NP_001129586.1:p.Arg375Ter
  • NP_001340122.2:p.Arg514Ter
  • NP_001340123.1:p.Arg438Ter
  • NP_001340124.1:p.Arg375Ter
  • NP_001340125.1:p.Arg462Ter
  • NP_001340126.2:p.Arg460Ter
  • NP_001340127.2:p.Arg460Ter
  • NP_001340128.2:p.Arg397Ter
  • NP_001340129.1:p.Arg340Ter
  • NP_001361618.1:p.Arg488Ter
  • NP_001361620.1:p.Arg375Ter
  • NP_001361621.1:p.Arg375Ter
  • NP_001361622.1:p.Arg375Ter
  • NP_001361624.1:p.Arg362Ter
  • NP_009102.3:p.Arg514Ter
  • NP_009102.4:p.Arg514Ter
  • LRG_842t1:c.1540C>T
  • LRG_842t2:c.1474C>T
  • LRG_842p1:p.Arg514Ter
  • LRG_842p2:p.Arg492Ter
  • NC_000009.11:g.134394332C>T
  • NP_009102.3:p.Arg514*
  • NR_148391.2:n.1508C>T
  • NR_148392.2:n.1726C>T
  • NR_148393.2:n.1647C>T
  • NR_148394.2:n.1401C>T
  • NR_148395.2:n.1799C>T
  • NR_148396.2:n.1433C>T
  • NR_148397.2:n.1558C>T
  • NR_148398.2:n.1513C>T
  • NR_148399.2:n.2039C>T
  • NR_148400.2:n.1638C>T
Protein change:
R340*; ARG514TER
Links:
OMIM: 607423.0008; dbSNP: rs119462985
NCBI 1000 Genomes Browser:
rs119462985
Molecular consequence:
  • NM_001374690.1:c.1365+408C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NR_148391.2:n.1508C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.1726C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.1647C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.1401C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.1799C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.1433C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.1558C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.1513C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.2039C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.1638C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001077365.2:c.1474C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001077366.2:c.1312C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001136113.2:c.1474C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001136114.2:c.1123C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353193.2:c.1540C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353194.2:c.1312C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353195.2:c.1123C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353196.2:c.1384C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353197.2:c.1378C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353198.2:c.1378C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353199.2:c.1189C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353200.2:c.1018C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374689.1:c.1462C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374691.1:c.1123C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374692.1:c.1123C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374693.1:c.1123C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374695.1:c.1084C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_007171.3:c.1540C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_007171.4:c.1540C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000226310EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Pathogenic
(Mar 20, 2014)
germlineclinical testing

Citation Link,

SCV000890215GeneDxcriteria provided, single submitter
Pathogenic
(Aug 21, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000226310.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000890215.1

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

Description

The R514X nonsense variant in the POMT1 gene has been reported previously in the homozygous state in an individual with a clinical diagnosis of Walker-Warburg syndrome (Yis et al., 2007). The R514X variant has also been reported along with a second POMT1 variant in unrelated individuals with congenital muscular dystrophy, microcephaly, and intellectual disability with variable additional findings (D'Amico et al., 2006; van Reeuwijk et al., 2006). This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R514X variant is not observed in large population cohorts (Lek et al., 2016). We interpret R514X as a pathogenic variant.

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

Last Updated: Feb 27, 2021

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