NM_024312.5(GNPTAB):c.1186G>T (p.Glu396Ter) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 27, 2021
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:: RCV001903278.4

Allele description [Variation Report for NM_024312.5(GNPTAB):c.1186G>T (p.Glu396Ter)]

NM_024312.5(GNPTAB):c.1186G>T (p.Glu396Ter)

Gene:

GNPTAB:N-acetylglucosamine-1-phosphate transferase subunits alpha and beta [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q23.2

Genomic location:

Preferred name:

NM_024312.5(GNPTAB):c.1186G>T (p.Glu396Ter)

HGVS:

NC_000012.12:g.101770119C>A
NG_021243.1:g.65749G>T
NM_024312.5:c.1186G>TMANE SELECT
NP_077288.2:p.Glu396Ter
NC_000012.11:g.102163897C>A

Protein change:

E396*

Links:

dbSNP: rs1245543262

NCBI 1000 Genomes Browser:

rs1245543262

Molecular consequence:

NM_024312.5:c.1186G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Mucolipidosis type II
Synonyms:: ML II ALPHA/BETA; I cell disease; Mucolipidosis 2; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009650; MedGen: C2673377; Orphanet: 576; OMIM: 252500

Name:: Pseudo-Hurler polydystrophy (ML3)
Synonyms:: ML III; ML III ALPHA/BETA; Mucolipidosis type 3A; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0018931; MedGen: C0033788; Orphanet: 577; OMIM: 252600

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002161117	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 27, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19617216, 25107912, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002161117

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 27, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Phenotype and genotype in mucolipidoses II and III alpha/beta: a study of 61 probands.

Cathey SS, Leroy JG, Wood T, Eaves K, Simensen RJ, Kudo M, Stevenson RE, Friez MJ.

J Med Genet. 2010 Jan;47(1):38-48. doi: 10.1136/jmg.2009.067736. Epub 2009 Jul 16.

PubMed [citation]

PMID:: 19617216
PMCID:: PMC3712854

A novel mouse model of a patient mucolipidosis II mutation recapitulates disease pathology.

Paton L, Bitoun E, Kenyon J, Priestman DA, Oliver PL, Edwards B, Platt FM, Davies KE.

J Biol Chem. 2014 Sep 26;289(39):26709-26721. doi: 10.1074/jbc.M114.586156. Epub 2014 Aug 8.

PubMed [citation]

PMID:: 25107912
PMCID:: PMC4175314

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002161117.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with GNPTAB-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Glu396*) in the GNPTAB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GNPTAB are known to be pathogenic (PMID: 19617216, 25107912).

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

Last Updated: Sep 29, 2024

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