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NM_001077365.2(POMT1):c.1837_1852dup (p.Gly618fs) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 30, 2019
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:
RCV000811436.9

Allele description [Variation Report for NM_001077365.2(POMT1):c.1837_1852dup (p.Gly618fs)]

NM_001077365.2(POMT1):c.1837_1852dup (p.Gly618fs)

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.1837_1852dup (p.Gly618fs)
HGVS:
  • NC_000009.12:g.131522058_131522073dup
  • NG_008896.1:g.24157_24172dup
  • NM_001077365.2:c.1837_1852dupMANE SELECT
  • NM_001077366.2:c.1675_1690dup
  • NM_001136113.2:c.1837_1852dup
  • NM_001136114.2:c.1486_1501dup
  • NM_001353193.2:c.1903_1918dup
  • NM_001353194.2:c.1675_1690dup
  • NM_001353195.2:c.1486_1501dup
  • NM_001353196.2:c.1747_1762dup
  • NM_001353197.2:c.1741_1756dup
  • NM_001353198.2:c.1741_1756dup
  • NM_001353199.2:c.1552_1567dup
  • NM_001353200.2:c.1381_1396dup
  • NM_001374689.1:c.1825_1840dup
  • NM_001374690.1:c.1618_1633dup
  • NM_001374691.1:c.1486_1501dup
  • NM_001374692.1:c.1486_1501dup
  • NM_001374693.1:c.1486_1501dup
  • NM_001374695.1:c.1447_1462dup
  • NM_007171.4:c.1903_1918dup
  • NP_001070833.1:p.Gly618fs
  • NP_001070834.1:p.Gly564fs
  • NP_001129585.1:p.Gly618fs
  • NP_001129586.1:p.Gly501fs
  • NP_001340122.2:p.Gly640fs
  • NP_001340123.1:p.Gly564fs
  • NP_001340124.1:p.Gly501fs
  • NP_001340125.1:p.Gly588fs
  • NP_001340126.2:p.Gly586fs
  • NP_001340127.2:p.Gly586fs
  • NP_001340128.2:p.Gly523fs
  • NP_001340129.1:p.Gly466fs
  • NP_001361618.1:p.Gly614fs
  • NP_001361619.1:p.Gly545fs
  • NP_001361620.1:p.Gly501fs
  • NP_001361621.1:p.Gly501fs
  • NP_001361622.1:p.Gly501fs
  • NP_001361624.1:p.Gly488fs
  • NP_009102.4:p.Gly640fs
  • LRG_842t1:c.1903_1918dup
  • LRG_842t2:c.1837_1852dup
  • LRG_842p1:p.Gly640fs
  • LRG_842p2:p.Gly618fs
  • NC_000009.11:g.134397437_134397438insCTGGCTGCGCTGGGTG
  • NC_000009.11:g.134397445_134397460dup
  • NM_007171.3:c.1903_1918dup16
  • NR_148391.2:n.1871_1886dup
  • NR_148392.2:n.2089_2104dup
  • NR_148393.2:n.2010_2025dup
  • NR_148394.2:n.1764_1779dup
  • NR_148395.2:n.2162_2177dup
  • NR_148396.2:n.1796_1811dup
  • NR_148397.2:n.1921_1936dup
  • NR_148398.2:n.1876_1891dup
  • NR_148399.2:n.2402_2417dup
  • NR_148400.2:n.2001_2016dup
Protein change:
G466fs
Links:
dbSNP: rs1315540509
NCBI 1000 Genomes Browser:
rs1315540509
Molecular consequence:
  • NM_001077365.2:c.1837_1852dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001077366.2:c.1675_1690dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001136113.2:c.1837_1852dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001136114.2:c.1486_1501dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353193.2:c.1903_1918dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353194.2:c.1675_1690dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353195.2:c.1486_1501dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353196.2:c.1747_1762dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353197.2:c.1741_1756dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353198.2:c.1741_1756dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353199.2:c.1552_1567dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353200.2:c.1381_1396dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374689.1:c.1825_1840dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374690.1:c.1618_1633dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374691.1:c.1486_1501dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374692.1:c.1486_1501dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374693.1:c.1486_1501dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374695.1:c.1447_1462dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_007171.4:c.1903_1918dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_148391.2:n.1871_1886dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.2089_2104dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.2010_2025dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.1764_1779dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.2162_2177dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.1796_1811dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.1921_1936dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.1876_1891dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.2402_2417dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.2001_2016dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Autosomal recessive limb-girdle muscular dystrophy type 2K
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 1; MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2K; Limb-girdle muscular dystrophy-dystroglycanopathy, type C1
Identifiers:
MONDO: MONDO:0012248; MedGen: C1836373; Orphanet: 86812; OMIM: 609308
Name:
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1 (MDDGB1)
Synonyms:
MUSCULAR DYSTROPHY, CONGENITAL, POMT1-RELATED; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL DEVELOPMENT), TYPE B, 1
Identifiers:
MONDO: MONDO:0013159; MedGen: C5436962; OMIM: 613155
Name:
Walker-Warburg congenital muscular dystrophy
Synonyms:
Muscular dystrophy-dystroglycanopathy, type A; Walker-Warburg syndrome
Identifiers:
MONDO: MONDO:0000171; MedGen: C0265221; Orphanet: 899; OMIM: PS236670

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000951703Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Apr 30, 2019) 		germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Mutations in the O-mannosyltransferase gene POMT1 give rise to the severe neuronal migration disorder Walker-Warburg syndrome.

Beltrán-Valero de Bernabé D, Currier S, Steinbrecher A, Celli J, van Beusekom E, van der Zwaag B, Kayserili H, Merlini L, Chitayat D, Dobyns WB, Cormand B, Lehesjoki AE, Cruces J, Voit T, Walsh CA, van Bokhoven H, Brunner HG.

Am J Hum Genet. 2002 Nov;71(5):1033-43. Epub 2002 Oct 4.

PubMed [citation]
PMID:
12369018
PMCID:
PMC419999

Cobblestone lissencephaly: neuropathological subtypes and correlations with genes of dystroglycanopathies.

Devisme L, Bouchet C, Gonzalès M, Alanio E, Bazin A, Bessières B, Bigi N, Blanchet P, Bonneau D, Bonnières M, Bucourt M, Carles D, Clarisse B, Delahaye S, Fallet-Bianco C, Figarella-Branger D, Gaillard D, Gasser B, Delezoide AL, Guimiot F, Joubert M, Laurent N, et al.

Brain. 2012 Feb;135(Pt 2):469-82. doi: 10.1093/brain/awr357. Epub 2012 Feb 9.

PubMed [citation]
PMID:
22323514
See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000951703.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

This sequence change results in a premature translational stop signal in the POMT1 gene (p.Gly640Alafs*96). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 108 amino acids of the POMT1 protein. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with POMT1-related disease. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. This variant disrupts the C-terminus of the POMT1 protein. Other variant(s) that disrupt this region (p.Asp723Glyfs*8) have been determined to be pathogenic (PMID: 12369018, 22323514, 17559086, 16575835, 24491487, 24304607). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024