NM_017739.4(POMGNT1):c.74G>A (p.Trp25Ter) AND Hydrocephalus

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 22, 2022
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:: RCV002466682.2

Allele description [Variation Report for NM_017739.4(POMGNT1):c.74G>A (p.Trp25Ter)]

NM_017739.4(POMGNT1):c.74G>A (p.Trp25Ter)

Gene:

POMGNT1:protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p34.1

Genomic location:

Preferred name:

NM_017739.4(POMGNT1):c.74G>A (p.Trp25Ter)

HGVS:

NC_000001.11:g.46197748C>T
NG_009205.3:g.27558G>A
NM_001243766.2:c.74G>A
NM_017739.4:c.74G>AMANE SELECT
NP_001230695.2:p.Trp25Ter
NP_060209.4:p.Trp25Ter
LRG_701t1:c.74G>A
LRG_701t2:c.74G>A
LRG_701:g.27558G>A
LRG_701p1:p.Trp25Ter
LRG_701p2:p.Trp25Ter
NC_000001.10:g.46663420C>T
NG_009205.2:g.27558G>A

Protein change:

W25*

Links:

dbSNP: rs1475539242

NCBI 1000 Genomes Browser:

rs1475539242

Molecular consequence:

NM_001243766.2:c.74G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_017739.4:c.74G>A - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Hydrocephalus (HYC)
Identifiers:: MONDO: MONDO:0001150; MedGen: C0020255; Human Phenotype Ontology: HP:0000238

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002761254	Clinical Genetics Laboratory, Noor Gene	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 22, 2022)	germline	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

SCV002761254

Clinical Genetics Laboratory, Noor Gene

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 22, 2022)

germline

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	germline	yes	1	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 Clinical Genetics Laboratory, Noor Gene, SCV002761254.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	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	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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