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NM_001077365.2(POMT1):c.2101dup (p.Asp701fs) AND Autosomal recessive limb-girdle muscular dystrophy

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 18, 2023
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:
RCV003398430.1

Allele description [Variation Report for NM_001077365.2(POMT1):c.2101dup (p.Asp701fs)]

NM_001077365.2(POMT1):c.2101dup (p.Asp701fs)

Gene:
POMT1:protein O-mannosyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
9q34.13
Genomic location:
Preferred name:
NM_001077365.2(POMT1):c.2101dup (p.Asp701fs)
Other names:
NM_001077365.2(POMT1):c.2101dup; p.Asp701fs
HGVS:
  • NC_000009.12:g.131523029dup
  • NG_008896.1:g.25128dup
  • NM_001077365.2:c.2101dupMANE SELECT
  • NM_001077366.2:c.1939dup
  • NM_001136113.2:c.2101dup
  • NM_001136114.2:c.1750dup
  • NM_001353193.2:c.2167dup
  • NM_001353194.2:c.1939dup
  • NM_001353195.2:c.1750dup
  • NM_001353196.2:c.2011dup
  • NM_001353197.2:c.2005dup
  • NM_001353198.2:c.2005dup
  • NM_001353199.2:c.1816dup
  • NM_001353200.2:c.1645dup
  • NM_001374689.1:c.2089dup
  • NM_001374690.1:c.1882dup
  • NM_001374691.1:c.1750dup
  • NM_001374692.1:c.1750dup
  • NM_001374693.1:c.1750dup
  • NM_001374695.1:c.1711dup
  • NM_007171.4:c.2167dup
  • NP_001070833.1:p.Asp701fs
  • NP_001070834.1:p.Asp647fs
  • NP_001129585.1:p.Asp701fs
  • NP_001129586.1:p.Asp584fs
  • NP_001340122.2:p.Asp723fs
  • NP_001340123.1:p.Asp647fs
  • NP_001340124.1:p.Asp584fs
  • NP_001340125.1:p.Asp671fs
  • NP_001340126.2:p.Asp669fs
  • NP_001340127.2:p.Asp669fs
  • NP_001340128.2:p.Asp606fs
  • NP_001340129.1:p.Asp549fs
  • NP_001361618.1:p.Asp697fs
  • NP_001361619.1:p.Asp628fs
  • NP_001361620.1:p.Asp584fs
  • NP_001361621.1:p.Asp584fs
  • NP_001361622.1:p.Asp584fs
  • NP_001361624.1:p.Asp571fs
  • NP_009102.3:p.Asp723fs
  • NP_009102.4:p.Asp723fs
  • LRG_842t1:c.2167dup
  • LRG_842t2:c.2101dup
  • LRG_842p1:p.Asp723fs
  • LRG_842p2:p.Asp701fs
  • NC_000009.11:g.134398412_134398413insG
  • NC_000009.11:g.134398416dup
  • NM_007171.3:c.2167dup
  • NM_007171.3:c.2167dupG
  • NM_007171.4:c.2167dupG
  • NR_148391.2:n.2135dup
  • NR_148392.2:n.2353dup
  • NR_148393.2:n.2274dup
  • NR_148394.2:n.2028dup
  • NR_148395.2:n.2426dup
  • NR_148396.2:n.2060dup
  • NR_148397.2:n.2185dup
  • NR_148398.2:n.2140dup
  • NR_148399.2:n.2666dup
  • NR_148400.2:n.2265dup
  • p.D723GfsX8
Protein change:
D549fs
Links:
OMIM: 607423.0018; dbSNP: rs398124245
NCBI 1000 Genomes Browser:
rs398124245
Molecular consequence:
  • NM_001077365.2:c.2101dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001077366.2:c.1939dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001136113.2:c.2101dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001136114.2:c.1750dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353193.2:c.2167dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353194.2:c.1939dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353195.2:c.1750dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353196.2:c.2011dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353197.2:c.2005dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353198.2:c.2005dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353199.2:c.1816dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353200.2:c.1645dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374689.1:c.2089dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374690.1:c.1882dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374691.1:c.1750dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374692.1:c.1750dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374693.1:c.1750dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374695.1:c.1711dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_007171.4:c.2167dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_148391.2:n.2135dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.2353dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.2274dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.2028dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.2426dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.2060dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.2185dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.2140dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.2666dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.2265dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Autosomal recessive limb-girdle muscular dystrophy
Identifiers:
MONDO: MONDO:0015152; MedGen: C2931907; OMIM: PS253600

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004121811Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Pathogenic
(Oct 18, 2023) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

Nothing to display

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004121811.1

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

Description

Variant summary: POMT1 c.2167dupG (p.Asp723GlyfsX8) results in a premature termination codon in the last exon affecting the last 26 amino acids of the encoded POMT1 protein. Although nonsense mediated decay is not predicted to occur, variants downstream of this position have been classified as pathogenic in ClinVar. The variant allele was found at a frequency of 0.00016 in 248716 control chromosomes. c.2167dupG has been reported in the literature in individuals affected with muscular dystrophy including Walker-Warburg syndrome (e.g. BeltranValterodeBernabe_2002). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 12369018). 13 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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

Last Updated: Nov 18, 2024