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NM_017739.4(POMGNT1):c.1895+1G>T AND Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Mar 18, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001810416.12

Allele description [Variation Report for NM_017739.4(POMGNT1):c.1895+1G>T]

NM_017739.4(POMGNT1):c.1895+1G>T

Genes:
POMGNT1:protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) [Gene - OMIM - HGNC]
TSPAN1:tetraspanin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p34.1
Genomic location:
Preferred name:
NM_017739.4(POMGNT1):c.1895+1G>T
HGVS:
  • NC_000001.11:g.46189457C>A
  • NG_009205.3:g.35849G>T
  • NM_001243766.2:c.1869+27G>T
  • NM_001290129.2:c.1829+1G>T
  • NM_001290130.2:c.1466+1G>T
  • NM_001410783.1:c.1895+1G>T
  • NM_017739.4:c.1895+1G>TMANE SELECT
  • LRG_701t1:c.1869+27G>T
  • LRG_701t2:c.1895+1G>T
  • LRG_701:g.35849G>T
  • NC_000001.10:g.46655129C>A
  • NM_001290129.1:c.1829+1G>T
  • NM_017739.3:c.1895+1G>T
Links:
dbSNP: rs386834024
NCBI 1000 Genomes Browser:
rs386834024
Molecular consequence:
  • NM_001243766.2:c.1869+27G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001290129.2:c.1829+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001290130.2:c.1466+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001410783.1:c.1895+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_017739.4:c.1895+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3
Synonyms:
WALKER-WARBURG SYNDROME OR MUSCLE-EYE-BRAIN DISEASE, POMGNT1-RELATED; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 3; Congenital muscular dystrophy-dystroglycanopathy with brain and eye anomalies, type A3
Identifiers:
MONDO: MONDO:0009667; MedGen: C3151519; OMIM: 253280

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002060325Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))		Pathogenic
(Oct 27, 2021) 		unknownclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link,

SCV004205952Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Mar 18, 2024) 		unknownclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Congenital muscular dystrophies in the UK population: Clinical and molecular spectrum of a large cohort diagnosed over a 12-year period.

Sframeli M, Sarkozy A, Bertoli M, Astrea G, Hudson J, Scoto M, Mein R, Yau M, Phadke R, Feng L, Sewry C, Fen ANS, Longman C, McCullagh G, Straub V, Robb S, Manzur A, Bushby K, Muntoni F.

Neuromuscul Disord. 2017 Sep;27(9):793-803. doi: 10.1016/j.nmd.2017.06.008. Epub 2017 Jun 16.

PubMed [citation]
PMID:
28688748

Novel POMGNT1 point mutations and intragenic rearrangements associated with muscle-eye-brain disease.

Saredi S, Ardissone A, Ruggieri A, Mottarelli E, Farina L, Rinaldi R, Silvestri E, Gandioli C, D'Arrigo S, Salerno F, Morandi L, Grammatico P, Pantaleoni C, Moroni I, Mora M.

J Neurol Sci. 2012 Jul 15;318(1-2):45-50. doi: 10.1016/j.jns.2012.04.008. Epub 2012 May 2.

PubMed [citation]
PMID:
22554691
PMCID:
PMC3405532
See all PubMed Citations (6)

Details of each submission

From Myriad Genetics, Inc., SCV002060325.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

NM_017739.3(POMGNT1):c.1895+1G>T is a canonical splice variant classified as pathogenic in the context of muscle-eye-brain disease. c.1895+1G>T has been observed in cases with relevant disease (PMID: 15466003, 19299310, 22323514, 28688748, 22554691). Functional assessments of this variant are available in the literature (PMID: 22554691). c.1895+1G>T has been observed in population frequency databases (gnomAD: FIN 0.02%). In summary, NM_017739.3(POMGNT1):c.1895+1G>T is a canonical splice variant that has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

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

From Baylor Genetics, SCV004205952.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024