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NM_001077365.2(POMT1):c.1364del (p.Lys455fs) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 5, 2022
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:
RCV002037840.4

Allele description [Variation Report for NM_001077365.2(POMT1):c.1364del (p.Lys455fs)]

NM_001077365.2(POMT1):c.1364del (p.Lys455fs)

Gene:
POMT1:protein O-mannosyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q34.13
Genomic location:
Preferred name:
NM_001077365.2(POMT1):c.1364del (p.Lys455fs)
HGVS:
  • NC_000009.12:g.131518536del
  • NG_008896.2:g.20635del
  • NM_001077365.2:c.1364delMANE SELECT
  • NM_001077366.2:c.1202del
  • NM_001136113.2:c.1364del
  • NM_001136114.2:c.1013del
  • NM_001353193.2:c.1430del
  • NM_001353194.2:c.1202del
  • NM_001353195.2:c.1013del
  • NM_001353196.2:c.1274del
  • NM_001353197.2:c.1268del
  • NM_001353198.2:c.1268del
  • NM_001353199.2:c.1079del
  • NM_001353200.2:c.908del
  • NM_001374689.1:c.1352del
  • NM_001374690.1:c.1364del
  • NM_001374691.1:c.1013del
  • NM_001374692.1:c.1013del
  • NM_001374693.1:c.1013del
  • NM_001374695.1:c.974del
  • NM_007171.4:c.1430del
  • NP_001070833.1:p.Lys455fs
  • NP_001070834.1:p.Lys401fs
  • NP_001129585.1:p.Lys455fs
  • NP_001129586.1:p.Lys338fs
  • NP_001340122.2:p.Lys477fs
  • NP_001340123.1:p.Lys401fs
  • NP_001340124.1:p.Lys338fs
  • NP_001340125.1:p.Lys425fs
  • NP_001340126.2:p.Lys423fs
  • NP_001340127.2:p.Lys423fs
  • NP_001340128.2:p.Lys360fs
  • NP_001340129.1:p.Lys303fs
  • NP_001361618.1:p.Lys451fs
  • NP_001361619.1:p.Lys455fs
  • NP_001361620.1:p.Lys338fs
  • NP_001361621.1:p.Lys338fs
  • NP_001361622.1:p.Lys338fs
  • NP_001361624.1:p.Lys325fs
  • NP_009102.4:p.Lys477fs
  • LRG_842t1:c.1430del
  • LRG_842t2:c.1364del
  • LRG_842:g.20635del
  • LRG_842p1:p.Lys477fs
  • LRG_842p2:p.Lys455fs
  • NC_000009.11:g.134393921del
  • NC_000009.11:g.134393923del
  • NG_008896.1:g.20635del
  • NR_148391.2:n.1398del
  • NR_148392.2:n.1616del
  • NR_148393.2:n.1398del
  • NR_148394.2:n.1291del
  • NR_148395.2:n.1550del
  • NR_148396.2:n.1184del
  • NR_148397.2:n.1448del
  • NR_148398.2:n.1403del
  • NR_148399.2:n.1790del
  • NR_148400.2:n.1389del
Protein change:
K303fs
Links:
dbSNP: rs1472946513
NCBI 1000 Genomes Browser:
rs1472946513
Molecular consequence:
  • NM_001077365.2:c.1364del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001077366.2:c.1202del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001136113.2:c.1364del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001136114.2:c.1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353193.2:c.1430del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353194.2:c.1202del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353195.2:c.1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353196.2:c.1274del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353197.2:c.1268del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353198.2:c.1268del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353199.2:c.1079del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001353200.2:c.908del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374689.1:c.1352del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374690.1:c.1364del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374691.1:c.1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374692.1:c.1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374693.1:c.1013del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374695.1:c.974del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_007171.4:c.1430del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_148391.2:n.1398del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.1616del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.1398del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.1291del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.1550del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.1184del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.1448del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.1403del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.1790del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.1389del - 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
SCV002230147Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 5, 2022) 		germlineclinical testing

PubMed (4)
[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

Mutations in POMT1 are found in a minority of patients with Walker-Warburg syndrome.

Currier SC, Lee CK, Chang BS, Bodell AL, Pai GS, Job L, Lagae LG, Al-Gazali LI, Eyaid WM, Enns G, Dobyns WB, Walsh CA.

Am J Med Genet A. 2005 Feb 15;133A(1):53-7.

PubMed [citation]
PMID:
15637732
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002230147.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1453137). This variant has not been reported in the literature in individuals affected with POMT1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys477Serfs*2) in the POMT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in POMT1 are known to be pathogenic (PMID: 12369018, 15637732, 16575835).

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

Last Updated: Sep 29, 2024