NM_024312.5(GNPTAB):c.2693del (p.Lys898fs) AND Pseudo-Hurler polydystrophy

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jul 28, 2016
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:: RCV000032323.3

Allele description [Variation Report for NM_024312.5(GNPTAB):c.2693del (p.Lys898fs)]

NM_024312.5(GNPTAB):c.2693del (p.Lys898fs)

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.2693del (p.Lys898fs)

HGVS:

NC_000012.12:g.101764231del
NG_021243.1:g.71644del
NM_024312.5:c.2693delMANE SELECT
NP_077288.2:p.Lys898fs
NC_000012.11:g.102158002del
NC_000012.11:g.102158009del
NM_024312.4:c.2693delA
NM_024312.5:c.2693delAMANE SELECT

Protein change:

K898fs

Links:

dbSNP: rs281864999

NCBI 1000 Genomes Browser:

rs281864999

Molecular consequence:

NM_024312.5:c.2693del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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
SCV000055968	GeneReviews	no classification provided	not provided	unknown	literature only	PubMed (2) [See all records that cite these PMIDs] 19197337, 20301728
SCV000699478	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Jul 28, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] LabCorp Variant Classification Summary - May 2015.docx Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000055968

GeneReviews

no classification provided

not provided

unknown

literature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000699478

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Jul 28, 2016)

germline

clinical testing

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

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

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
not provided	unknown	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

GNPTAB-Related Disorders.

Leroy JG, Cathey SS, Friez MJ.

2008 Aug 26 [updated 2019 Aug 29]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]

PMID:: 20301728

Mucolipidosis II and III alpha/beta: mutation analysis of 40 Japanese patients showed genotype-phenotype correlation.

Otomo T, Muramatsu T, Yorifuji T, Okuyama T, Nakabayashi H, Fukao T, Ohura T, Yoshino M, Tanaka A, Okamoto N, Inui K, Ozono K, Sakai N.

J Hum Genet. 2009 Mar;54(3):145-51. doi: 10.1038/jhg.2009.3. Epub 2009 Feb 6.

PubMed [citation]

PMID:: 19197337

Details of each submission

From GeneReviews, SCV000055968.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699478.1

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

Description

Variant summary: The GNPTAB c.2693delA (p.Lys898Serfs) variant results in a premature termination codon, predicted to cause a truncated or absent GNPTAB protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant of interest was not found in controls (ExAC, 1000 Gs or ESP) and has been reported in one affected individual who was diagnosed with ML III and was compound heterozygous for the variant of interest and an exon 2 duplication. GeneReviews classifies the variant as "pathogenic." Therefore, taking all available lines of evidence into consideration the varinat of interest has been classified as Pathogenic.

#	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: Jun 23, 2024

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