NM_024312.5(GNPTAB):c.1345del (p.Asp449fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 16, 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:: RCV003805582.2

Allele description [Variation Report for NM_024312.5(GNPTAB):c.1345del (p.Asp449fs)]

NM_024312.5(GNPTAB):c.1345del (p.Asp449fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

12q23.2

Genomic location:

Preferred name:

NM_024312.5(GNPTAB):c.1345del (p.Asp449fs)

HGVS:

NC_000012.12:g.101768101del
NG_021243.1:g.67768del
NM_024312.5:c.1345delMANE SELECT
NP_077288.2:p.Asp449fs
NC_000012.11:g.102161878del
NC_000012.11:g.102161879del

Protein change:

D449fs

Molecular consequence:

NM_024312.5:c.1345del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Recent activity

Clear Turn Off Turn On

Mus musculus family with sequence similarity 176, member A, mRNA (cDNA clone MGC...
Mus musculus family with sequence similarity 176, member A, mRNA (cDNA clone MGC:37042 IMAGE:4950341), complete cds
gi|20072072|gb|BC027150.1|

Nucleotide
origin of replication complex subunit 2 [Cucumis sativus]
origin of replication complex subunit 2 [Cucumis sativus]
gi|449470053|ref|XP_004152733.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004589059	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 16, 2022)	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

SCV004589059

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 16, 2022)

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, SCV004589059.1

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

Description

This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Asp449Metfs*51) 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). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with GNPTAB-related conditions.

#	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

ClinVar

Relating variation to medicine