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NM_001077365.2(POMT1):c.697_699del (p.Asn233del) AND POMT1-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 15, 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:
RCV004530476.1

Allele description [Variation Report for NM_001077365.2(POMT1):c.697_699del (p.Asn233del)]

NM_001077365.2(POMT1):c.697_699del (p.Asn233del)

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.697_699del (p.Asn233del)
HGVS:
  • NC_000009.12:g.131509994_131509996del
  • NG_008896.1:g.12093_12095del
  • NM_001077365.2:c.697_699delMANE SELECT
  • NM_001077366.2:c.535_537del
  • NM_001136113.2:c.697_699del
  • NM_001136114.2:c.346_348del
  • NM_001353193.2:c.697_699del
  • NM_001353194.2:c.535_537del
  • NM_001353195.2:c.346_348del
  • NM_001353196.2:c.607_609del
  • NM_001353197.2:c.535_537del
  • NM_001353198.2:c.535_537del
  • NM_001353199.2:c.346_348del
  • NM_001353200.2:c.241_243del
  • NM_001374689.1:c.535_537del
  • NM_001374690.1:c.697_699del
  • NM_001374691.1:c.346_348del
  • NM_001374692.1:c.346_348del
  • NM_001374693.1:c.535_537del
  • NM_001374695.1:c.241_243del
  • NM_007171.4:c.697_699del
  • NP_001070833.1:p.Asn233del
  • NP_001070834.1:p.Asn179del
  • NP_001129585.1:p.Asn233del
  • NP_001129586.1:p.Asn116del
  • NP_001129586.1:p.Asn116del
  • NP_001340122.2:p.Asn233del
  • NP_001340123.1:p.Asn179del
  • NP_001340124.1:p.Asn116del
  • NP_001340125.1:p.Asn203del
  • NP_001340126.2:p.Asn179del
  • NP_001340127.2:p.Asn179del
  • NP_001340128.2:p.Asn116del
  • NP_001340129.1:p.Asn81del
  • NP_001361618.1:p.Asn179del
  • NP_001361619.1:p.Asn233del
  • NP_001361620.1:p.Asn116del
  • NP_001361621.1:p.Asn116del
  • NP_001361622.1:p.Asn179del
  • NP_001361624.1:p.Asn81del
  • NP_009102.4:p.Asn233del
  • LRG_842t1:c.697_699del
  • LRG_842t2:c.697_699del
  • LRG_842p1:p.Asn233del
  • LRG_842p2:p.Asn233del
  • NC_000009.11:g.134385381_134385383del
  • NM_001136114.1:c.346_348del
  • NM_007171.3:c.697_699del
  • NM_007171.3:c.697_699delAAT
  • NR_148391.2:n.731_733del
  • NR_148392.2:n.883_885del
  • NR_148393.2:n.731_733del
  • NR_148394.2:n.619_621del
  • NR_148395.2:n.883_885del
  • NR_148396.2:n.512_514del
  • NR_148397.2:n.776_778del
  • NR_148398.2:n.731_733del
  • NR_148399.2:n.1123_1125del
  • NR_148400.2:n.717_719del
Protein change:
N116del
Links:
dbSNP: rs761863400
NCBI 1000 Genomes Browser:
rs761863400
Molecular consequence:
  • NM_001077365.2:c.697_699del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001077366.2:c.535_537del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001136113.2:c.697_699del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001136114.2:c.346_348del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001353193.2:c.697_699del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001353194.2:c.535_537del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001353195.2:c.346_348del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001353196.2:c.607_609del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001353197.2:c.535_537del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001353198.2:c.535_537del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001353199.2:c.346_348del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001353200.2:c.241_243del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001374689.1:c.535_537del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001374690.1:c.697_699del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001374691.1:c.346_348del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001374692.1:c.346_348del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001374693.1:c.535_537del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001374695.1:c.241_243del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_007171.4:c.697_699del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NR_148391.2:n.731_733del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148392.2:n.883_885del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148393.2:n.731_733del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148394.2:n.619_621del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148395.2:n.883_885del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148396.2:n.512_514del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148397.2:n.776_778del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148398.2:n.731_733del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148399.2:n.1123_1125del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148400.2:n.717_719del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
POMT1-related disorder
Synonyms:
POMT1-Related Disorders; POMT1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004113368PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Feb 15, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot 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 PreventionGenetics, part of Exact Sciences, SCV004113368.1

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

Description

The POMT1 c.697_699delAAT variant is predicted to result in an in-frame deletion (p.Asn233del). The c.697_699delAAT nucleotides also reside at the end of exon 8 in alternative biologically relevant POMT1 transcripts (eg. NM_001077365.2) and deletion of these nucleotides is predicted to result in defective splicing by several in silico programs (Alamut Visual Plus v1.6.1). This variant was reported in the compound heterozygous state in an individual with a POMT1-related disorder (Table S2 - Bowling et al 2022. PubMed ID: 34930662). At PreventionGenetics, we have observed the c.697_699delAAT variant with a loss-of-function variant in POMT1 in a patient with suspected dystroglycanopathy (internal data). This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/9-134385380-CAAT-C). This variant is interpreted as likely pathogenic.

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

Last Updated: Jan 13, 2025