NM_001077365.2(POMT1):c.868C>T (p.Arg290Trp) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Dec 19, 2016)

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:
RCV000725271.2

Allele description [Variation Report for NM_001077365.2(POMT1):c.868C>T (p.Arg290Trp)]

NM_001077365.2(POMT1):c.868C>T (p.Arg290Trp)

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.868C>T (p.Arg290Trp)
HGVS:
  • NC_000009.12:g.131511349C>T
  • NG_008896.1:g.13448C>T
  • NM_001077365.2:c.868C>TMANE SELECT
  • NM_001077366.2:c.706C>T
  • NM_001136113.2:c.868C>T
  • NM_001136114.2:c.517C>T
  • NM_001353193.2:c.934C>T
  • NM_001353194.2:c.706C>T
  • NM_001353195.2:c.517C>T
  • NM_001353196.2:c.778C>T
  • NM_001353197.2:c.772C>T
  • NM_001353198.2:c.772C>T
  • NM_001353199.2:c.583C>T
  • NM_001353200.2:c.412C>T
  • NM_001374689.1:c.851C>T
  • NM_001374690.1:c.868C>T
  • NM_001374691.1:c.517C>T
  • NM_001374692.1:c.517C>T
  • NM_001374693.1:c.706C>T
  • NM_001374695.1:c.478C>T
  • NM_007171.3:c.934C>T
  • NM_007171.4:c.934C>T
  • NP_001070833.1:p.Arg290Trp
  • NP_001070834.1:p.Arg236Trp
  • NP_001129585.1:p.Arg290Trp
  • NP_001129586.1:p.Arg173Trp
  • NP_001340122.2:p.Arg312Trp
  • NP_001340123.1:p.Arg236Trp
  • NP_001340124.1:p.Arg173Trp
  • NP_001340125.1:p.Arg260Trp
  • NP_001340126.2:p.Arg258Trp
  • NP_001340127.2:p.Arg258Trp
  • NP_001340128.2:p.Arg195Trp
  • NP_001340129.1:p.Arg138Trp
  • NP_001361618.1:p.Ser284Leu
  • NP_001361619.1:p.Arg290Trp
  • NP_001361620.1:p.Arg173Trp
  • NP_001361621.1:p.Arg173Trp
  • NP_001361622.1:p.Arg236Trp
  • NP_001361624.1:p.Arg160Trp
  • NP_009102.3:p.Arg312Trp
  • NP_009102.4:p.Arg312Trp
  • LRG_842t1:c.934C>T
  • LRG_842t2:c.868C>T
  • LRG_842p1:p.Arg312Trp
  • LRG_842p2:p.Arg290Trp
  • NC_000009.11:g.134386736C>T
  • NR_148391.2:n.902C>T
  • NR_148392.2:n.1120C>T
  • NR_148393.2:n.902C>T
  • NR_148394.2:n.790C>T
  • NR_148395.2:n.1054C>T
  • NR_148396.2:n.683C>T
  • NR_148397.2:n.947C>T
  • NR_148398.2:n.902C>T
  • NR_148399.2:n.1294C>T
  • NR_148400.2:n.888C>T
Protein change:
R138W
Links:
dbSNP: rs886042627
NCBI 1000 Genomes Browser:
rs886042627
Molecular consequence:
  • NM_001077365.2:c.868C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077366.2:c.706C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136113.2:c.868C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136114.2:c.517C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353193.2:c.934C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353194.2:c.706C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353195.2:c.517C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353196.2:c.778C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353197.2:c.772C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353198.2:c.772C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353199.2:c.583C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353200.2:c.412C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374689.1:c.851C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374690.1:c.868C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374691.1:c.517C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374692.1:c.517C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374693.1:c.706C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374695.1:c.478C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007171.3:c.934C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007171.4:c.934C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148391.2:n.902C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.1120C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.902C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.790C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.1054C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.683C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.947C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.902C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.1294C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.888C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
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
SCV000335534EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Oct 22, 2015)
germlineclinical testing

Citation Link,

SCV000534415GeneDxcriteria provided, single submitter
Uncertain significance
(Dec 19, 2016)
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, SCV000335534.4

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

From GeneDx, SCV000534415.4

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

Description

The R312W variant in the POMT1 gene has not been published as a pathogenic variant, nor as a benign variant, to our knowledge. The R312W variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R312W 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. Therefore, we interpret R312W as a variant of uncertain significance.

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

Last Updated: Jul 7, 2021

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