NM_024312.5(GNPTAB):c.1120T>C (p.Phe374Leu) AND Mucolipidosis type II

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Mar 1, 2009
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000002905.5

Allele description [Variation Report for NM_024312.5(GNPTAB):c.1120T>C (p.Phe374Leu)]

NM_024312.5(GNPTAB):c.1120T>C (p.Phe374Leu)

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.1120T>C (p.Phe374Leu)

HGVS:

NC_000012.12:g.101770185A>G
NG_021243.1:g.65683T>C
NM_024312.5:c.1120T>CMANE SELECT
NP_077288.2:p.Phe374Leu
NC_000012.11:g.102163963A>G
NM_024312.4:c.1120T>C
Q3T906:p.Phe374Leu

Protein change:

F374L; PHE374LEU

Links:

UniProtKB: Q3T906#VAR_062807; OMIM: 607840.0015; dbSNP: rs137852900

NCBI 1000 Genomes Browser:

rs137852900

Molecular consequence:

NM_024312.5:c.1120T>C - missense variant - [Sequence Ontology: SO:0001583]

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000023063	OMIM	no assertion criteria provided	Pathogenic (Mar 1, 2009)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000055930	GeneReviews	no classification provided	not provided	unknown	literature only	PubMed (2) [See all records that cite these PMIDs] 19197337, 20301728

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000023063

OMIM

no assertion criteria provided

Pathogenic
(Mar 1, 2009)

germline

literature only

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

SCV000055930

GeneReviews

no classification provided

not provided

unknown

literature only

PubMed (2)
[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	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	unknown	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

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

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

Details of each submission

From OMIM, SCV000023063.1

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

Description

Otomo et al. (2009) identified a 1120T-C transition in exon 10 of the GNPTAB gene, resulting in a phe374-to-leu (F374L) substitution in 7 of 15 unrelated Japanese patients with mucolipidosis III (252600). Most were in compound heterozygosity with R1189X (607840.0004). Only 1 of 25 patients with a diagnosis of the more severe mucolipidosis II (252500) carried the F374L mutation; the second mutant allele in this patient was not identified. However, Otomo et al. (2009) stated that this patient had a relatively attenuated course, suggesting that F374L is associated with milder clinical manifestations. The F374L mutation occurred in 8 (10%) of 80 mutant alleles. Analysis of surrounding polymorphisms suggested a founder effect.

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

From GeneReviews, SCV000055930.2

#	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

Last Updated: Dec 17, 2022

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