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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002060325	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Pathogenic (Oct 27, 2021)	unknown	clinical testing	PubMed (5) [See all records that cite these PMIDs] 28688748, 22554691, 22323514, 15466003, 19299310 Citation Link,
SCV004205952	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 18, 2024)	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

SCV002060325

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))

Pathogenic
(Oct 27, 2021)

unknown

clinical testing

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

Citation Link,

SCV004205952

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 18, 2024)

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

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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	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

From Baylor Genetics, SCV004205952.2

#	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: Sep 8, 2024

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