NM_001077365.2(POMT1):c.1781G>A (p.Trp594Ter) AND Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Mar 6, 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:: RCV003472491.1

Allele description [Variation Report for NM_001077365.2(POMT1):c.1781G>A (p.Trp594Ter)]

NM_001077365.2(POMT1):c.1781G>A (p.Trp594Ter)

Gene:

POMT1:protein O-mannosyltransferase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_001077365.2(POMT1):c.1781G>A (p.Trp594Ter)

HGVS:

NC_000009.12:g.131521428G>A
NG_008896.2:g.23527G>A
NM_001077365.2:c.1781G>AMANE SELECT
NM_001077366.2:c.1619G>A
NM_001136113.2:c.1781G>A
NM_001136114.2:c.1430G>A
NM_001353193.2:c.1847G>A
NM_001353194.2:c.1619G>A
NM_001353195.2:c.1430G>A
NM_001353196.2:c.1691G>A
NM_001353197.2:c.1685G>A
NM_001353198.2:c.1685G>A
NM_001353199.2:c.1496G>A
NM_001353200.2:c.1325G>A
NM_001374689.1:c.1769G>A
NM_001374690.1:c.1562G>A
NM_001374691.1:c.1430G>A
NM_001374692.1:c.1430G>A
NM_001374693.1:c.1430G>A
NM_001374695.1:c.1391G>A
NM_001411024.1:c.650G>A
NM_007171.4:c.1847G>A
NP_001070833.1:p.Trp594Ter
NP_001070834.1:p.Trp540Ter
NP_001129585.1:p.Trp594Ter
NP_001129586.1:p.Trp477Ter
NP_001340122.2:p.Trp616Ter
NP_001340123.1:p.Trp540Ter
NP_001340124.1:p.Trp477Ter
NP_001340125.1:p.Trp564Ter
NP_001340126.2:p.Trp562Ter
NP_001340127.2:p.Trp562Ter
NP_001340128.2:p.Trp499Ter
NP_001340129.1:p.Trp442Ter
NP_001361618.1:p.Trp590Ter
NP_001361619.1:p.Trp521Ter
NP_001361620.1:p.Trp477Ter
NP_001361621.1:p.Trp477Ter
NP_001361622.1:p.Trp477Ter
NP_001361624.1:p.Trp464Ter
NP_001397953.1:p.Trp217Ter
NP_009102.4:p.Trp616Ter
LRG_842t1:c.1847G>A
LRG_842t2:c.1781G>A
LRG_842:g.23527G>A
LRG_842p1:p.Trp616Ter
LRG_842p2:p.Trp594Ter
NC_000009.11:g.134396815G>A
NR_148391.2:n.1815G>A
NR_148392.2:n.2033G>A
NR_148393.2:n.1954G>A
NR_148394.2:n.1708G>A
NR_148395.2:n.2106G>A
NR_148396.2:n.1740G>A
NR_148397.2:n.1865G>A
NR_148398.2:n.1820G>A
NR_148399.2:n.2346G>A
NR_148400.2:n.1945G>A

Protein change:

W217*

Molecular consequence:

NR_148391.2:n.1815G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.2033G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.1954G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.1708G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.2106G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148396.2:n.1740G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148397.2:n.1865G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.1820G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.2346G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148400.2:n.1945G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001077365.2:c.1781G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001077366.2:c.1619G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001136113.2:c.1781G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001136114.2:c.1430G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353193.2:c.1847G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353194.2:c.1619G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353195.2:c.1430G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353196.2:c.1691G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353197.2:c.1685G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353198.2:c.1685G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353199.2:c.1496G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001353200.2:c.1325G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374689.1:c.1769G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374690.1:c.1562G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374691.1:c.1430G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374692.1:c.1430G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374693.1:c.1430G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374695.1:c.1391G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001411024.1:c.650G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_007171.4:c.1847G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 (MDDGA1)
Synonyms:: Hydrocephalus, agyria and retinal dysplasia; Hard +/- E syndrome; Warburg syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009364; MedGen: C4284790; Orphanet: 588; Orphanet: 899; OMIM: 236670

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LSM5 LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated [Homo sa...
LSM5 LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated [Homo sapiens]
Gene ID:23658

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004204062	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 6, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004204062

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 6, 2023)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Baylor Genetics, SCV004204062.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 30, 2024

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