NM_001077365.2(POMT1):c.962_982del (p.Ser321_Met328delinsLeu) AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Jul 20, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001365714.1

Allele description [Variation Report for NM_001077365.2(POMT1):c.962_982del (p.Ser321_Met328delinsLeu)]

NM_001077365.2(POMT1):c.962_982del (p.Ser321_Met328delinsLeu)

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.962_982del (p.Ser321_Met328delinsLeu)
HGVS:
  • NC_000009.12:g.131511443_131511463del
  • NG_008896.1:g.13542_13562del
  • NG_008896.2:g.13542_13562del
  • NM_001077365.2:c.962_982delMANE SELECT
  • NM_001077366.2:c.800_820del
  • NM_001136113.2:c.962_982del
  • NM_001136114.2:c.611_631del
  • NM_001353193.2:c.1028_1048del
  • NM_001353194.2:c.800_820del
  • NM_001353195.2:c.611_631del
  • NM_001353196.2:c.872_892del
  • NM_001353197.2:c.866_886del
  • NM_001353198.2:c.866_886del
  • NM_001353199.2:c.677_697del
  • NM_001353200.2:c.506_526del
  • NM_001374689.1:c.945_965del
  • NM_001374690.1:c.962_982del
  • NM_001374691.1:c.611_631del
  • NM_001374692.1:c.611_631del
  • NM_001374693.1:c.800_820del
  • NM_001374695.1:c.572_592del
  • NM_007171.4:c.1028_1048del
  • NP_001070833.1:p.Ser321_Met328delinsLeu
  • NP_001070834.1:p.Ser267_Met274delinsLeu
  • NP_001129585.1:p.Ser321_Met328delinsLeu
  • NP_001129586.1:p.Ser204_Met211delinsLeu
  • NP_001340122.2:p.Ser343_Met350delinsLeu
  • NP_001340123.1:p.Ser267_Met274delinsLeu
  • NP_001340124.1:p.Ser204_Met211delinsLeu
  • NP_001340125.1:p.Ser291_Met298delinsLeu
  • NP_001340126.2:p.Ser289_Met296delinsLeu
  • NP_001340127.2:p.Ser289_Met296delinsLeu
  • NP_001340128.2:p.Ser226_Met233delinsLeu
  • NP_001340129.1:p.Ser169_Met176delinsLeu
  • NP_001361618.1:p.Pro316_His322del
  • NP_001361619.1:p.Ser321_Met328delinsLeu
  • NP_001361620.1:p.Ser204_Met211delinsLeu
  • NP_001361621.1:p.Ser204_Met211delinsLeu
  • NP_001361622.1:p.Ser267_Met274delinsLeu
  • NP_001361624.1:p.Ser191_Met198delinsLeu
  • NP_009102.4:p.Ser343_Met350delinsLeu
  • LRG_842t1:c.1028_1048del
  • LRG_842t2:c.962_982del
  • LRG_842:g.13542_13562del
  • LRG_842p1:p.Ser343_Met350delinsLeu
  • LRG_842p2:p.Ser321_Met328delinsLeu
  • NC_000009.11:g.134386830_134386850del
  • NR_148391.2:n.996_1016del
  • NR_148392.2:n.1214_1234del
  • NR_148393.2:n.996_1016del
  • NR_148394.2:n.884_904del
  • NR_148395.2:n.1148_1168del
  • NR_148396.2:n.777_797del
  • NR_148397.2:n.1041_1061del
  • NR_148398.2:n.996_1016del
  • NR_148399.2:n.1388_1408del
  • NR_148400.2:n.982_1002del
Molecular consequence:
  • NM_001374689.1:c.945_965del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001077365.2:c.962_982del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001077366.2:c.800_820del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001136113.2:c.962_982del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001136114.2:c.611_631del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001353193.2:c.1028_1048del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001353194.2:c.800_820del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001353195.2:c.611_631del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001353196.2:c.872_892del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001353197.2:c.866_886del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001353198.2:c.866_886del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001353199.2:c.677_697del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001353200.2:c.506_526del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001374690.1:c.962_982del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001374691.1:c.611_631del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001374692.1:c.611_631del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001374693.1:c.800_820del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_001374695.1:c.572_592del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NM_007171.4:c.1028_1048del - inframe_indel - [Sequence Ontology: SO:0001820]
  • NR_148391.2:n.996_1016del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.1214_1234del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.996_1016del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.884_904del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.1148_1168del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.777_797del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.1041_1061del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.996_1016del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.1388_1408del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.982_1002del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Limb-girdle muscular dystrophy-dystroglycanopathy, type C1 (MDDGC1)
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 1; MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2K; MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 11
Identifiers:
MONDO: MONDO:0012248; MedGen: C1836373; Orphanet: 86812; OMIM: 609308
Name:
Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B1 (MDDGB1)
Synonyms:
MUSCULAR DYSTROPHY, CONGENITAL, POMT1-RELATED; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL IMPAIRMENT), TYPE B, 1; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1
Identifiers:
MONDO: MONDO:0013159; MedGen: C3150415; OMIM: 613155
Name:
Walker-Warburg congenital muscular dystrophy (MDDGA1)
Synonyms:
HARD syndrome; 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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001561992Invitaecriteria provided, single submitter
Uncertain significance
(Jul 20, 2020)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001561992.1

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

Description

This variant, c.1028_1048del, results in the deletion of 8 amino acids of the POMT1 protein (p.Ser343_Met350delinsLeu), but otherwise preserves the integrity of the reading frame. 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 conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Jun 14, 2021

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