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NM_001077365.2(POMT1):c.132A>C (p.Glu44Asp) AND not provided

Germline classification:
Likely pathogenic (3 submissions)
Last evaluated:
Nov 11, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000177268.15

Allele description [Variation Report for NM_001077365.2(POMT1):c.132A>C (p.Glu44Asp)]

NM_001077365.2(POMT1):c.132A>C (p.Glu44Asp)

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.132A>C (p.Glu44Asp)
HGVS:
  • NC_000009.12:g.131506123A>C
  • NG_008896.1:g.8222A>C
  • NM_001077365.2:c.132A>CMANE SELECT
  • NM_001077366.2:c.-31A>C
  • NM_001136113.2:c.132A>C
  • NM_001136114.2:c.-122-280A>C
  • NM_001353193.2:c.132A>C
  • NM_001353194.2:c.-31A>C
  • NM_001353195.2:c.-122-280A>C
  • NM_001353196.2:c.123-280A>C
  • NM_001353197.2:c.-31A>C
  • NM_001353198.2:c.-31A>C
  • NM_001353199.2:c.-122-280A>C
  • NM_001353200.2:c.-80-280A>C
  • NM_001374689.1:c.-31A>C
  • NM_001374690.1:c.132A>C
  • NM_001374691.1:c.-71-1245A>C
  • NM_001374692.1:c.-71-1245A>C
  • NM_001374693.1:c.-31A>C
  • NM_001374695.1:c.-30+1783A>C
  • NM_007171.4:c.132A>C
  • NP_001070833.1:p.Glu44Asp
  • NP_001129585.1:p.Glu44Asp
  • NP_001340122.2:p.Glu44Asp
  • NP_001361619.1:p.Glu44Asp
  • NP_009102.3:p.Glu44Asp
  • NP_009102.3:p.Glu44Asp
  • NP_009102.4:p.Glu44Asp
  • LRG_842t1:c.132A>C
  • LRG_842t2:c.132A>C
  • LRG_842p1:p.Glu44Asp
  • LRG_842p2:p.Glu44Asp
  • NC_000009.11:g.134381510A>C
  • NM_007171.3:c.132A>C
  • NR_148391.2:n.166A>C
  • NR_148392.2:n.318A>C
  • NR_148393.2:n.166A>C
  • NR_148394.2:n.166A>C
  • NR_148395.2:n.318A>C
  • NR_148398.2:n.166A>C
  • NR_148399.2:n.558A>C
Protein change:
E44D
Links:
dbSNP: rs398124244
NCBI 1000 Genomes Browser:
rs398124244
Molecular consequence:
  • NM_001077366.2:c.-31A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353194.2:c.-31A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353197.2:c.-31A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353198.2:c.-31A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374689.1:c.-31A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001374693.1:c.-31A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001136114.2:c.-122-280A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353195.2:c.-122-280A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353196.2:c.123-280A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353199.2:c.-122-280A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353200.2:c.-80-280A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374691.1:c.-71-1245A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374692.1:c.-71-1245A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374695.1:c.-30+1783A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001077365.2:c.132A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136113.2:c.132A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353193.2:c.132A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374690.1:c.132A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007171.4:c.132A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148391.2:n.166A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.318A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.166A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.166A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.318A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.166A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.558A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
5

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000229112Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions)
Likely pathogenic
(Nov 27, 2013)
germlineclinical testing

Citation Link,

SCV002526472GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely pathogenic
(Apr 12, 2022)
germlineclinical testing

Citation Link,

SCV003813304Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Nov 11, 2022)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown5not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Eurofins Ntd Llc (ga), SCV000229112.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided5not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided5not providednot providednot provided

From GeneDx, SCV002526472.2

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

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27159402, 30564623)

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

From Revvity Omics, Revvity, SCV003813304.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 15, 2024