NM_032520.5(GNPTG):c.316G>A (p.Gly106Ser) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 9, 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:: RCV001062193.8

Allele description [Variation Report for NM_032520.5(GNPTG):c.316G>A (p.Gly106Ser)]

NM_032520.5(GNPTG):c.316G>A (p.Gly106Ser)

Gene:

GNPTG:N-acetylglucosamine-1-phosphate transferase subunit gamma [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_032520.5(GNPTG):c.316G>A (p.Gly106Ser)

HGVS:

NC_000016.10:g.1361954G>A
NG_016985.1:g.15056G>A
NG_033129.1:g.57751C>T
NM_032520.5:c.316G>AMANE SELECT
NP_115909.1:p.Gly106Ser
NC_000016.9:g.1411955G>A
NM_032520.4:c.316G>A
Q9UJJ9:p.Gly106Ser

Protein change:

G106S; GLY106SER

Links:

UniProtKB: Q9UJJ9#VAR_077164; OMIM: 607838.0006; dbSNP: rs137852885

NCBI 1000 Genomes Browser:

rs137852885

Molecular consequence:

NM_032520.5:c.316G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001226975	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 9, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 27038293, 15060128, 19370764, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001226975

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 9, 2022)

germline

clinical testing

PubMed (4)
[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

Mucolipidosis III GNPTG Missense Mutations Cause Misfolding of the γ Subunit of GlcNAc-1-Phosphotransferase.

van Meel E, Kornfeld S.

Hum Mutat. 2016 Jul;37(7):623-6. doi: 10.1002/humu.22993. Epub 2016 Apr 22.

PubMed [citation]

PMID:: 27038293
PMCID:: PMC4907843

Genomic organisation of the UDP-N-acetylglucosamine-1-phosphotransferase gamma subunit (GNPTAG) and its mutations in mucolipidosis III.

Raas-Rothschild A, Bargal R, Goldman O, Ben-Asher E, Groener JE, Toutain A, Stemmer E, Ben-Neriah Z, Flusser H, Beemer FA, Penttinen M, Olender T, Rein AJ, Bach G, Zeigler M.

J Med Genet. 2004 Apr;41(4):e52. No abstract available.

PubMed [citation]

PMID:: 15060128
PMCID:: PMC1735719

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001226975.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Experimental studies have shown that this missense change affects GNPTG function (PMID: 27038293). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 2799). This missense change has been observed in individual(s) with mucolipidosis III (PMID: 15060128, 19370764). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs137852885, gnomAD 0.002%). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 106 of the GNPTG protein (p.Gly106Ser).

#	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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