NM_032520.5(GNPTG):c.89_90del (p.Val30fs) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 30, 2020
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:: RCV001388650.6

Allele description

NM_032520.5(GNPTG):c.89_90del (p.Val30fs)

Genes:

LOC130058158:ATAC-STARR-seq lymphoblastoid silent region 6972 [Gene]
GNPTG:N-acetylglucosamine-1-phosphate transferase subunit gamma [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_032520.5(GNPTG):c.89_90del (p.Val30fs)

HGVS:

NC_000016.10:g.1352138_1352139del
NG_016985.1:g.5240_5241del
NM_032520.5:c.89_90delMANE SELECT
NP_115909.1:p.Val30fs
NC_000016.9:g.1402138_1402139del
NC_000016.9:g.1402139_1402140del

Protein change:

V30fs

Links:

dbSNP: rs1335120510

NCBI 1000 Genomes Browser:

rs1335120510

Molecular consequence:

NM_032520.5:c.89_90del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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docking protein 4 isoform 2 [Homo sapiens]
docking protein 4 isoform 2 [Homo sapiens]
gi|2030424417|ref|NP_001381584.1|

Protein
fractalkine isoform 1 precursor [Homo sapiens]
fractalkine isoform 1 precursor [Homo sapiens]
gi|4506857|ref|NP_002987.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001589723	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 30, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19370764, 20301784, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001589723

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 30, 2020)

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

Identification and molecular characterization of six novel mutations in the UDP-N-acetylglucosamine-1-phosphotransferase gamma subunit (GNPTG) gene in patients with mucolipidosis III gamma.

Persichetti E, Chuzhanova NA, Dardis A, Tappino B, Pohl S, Thomas NS, Rosano C, Balducci C, Paciotti S, Dominissini S, Montalvo AL, Sibilio M, Parini R, Rigoldi M, Di Rocco M, Parenti G, Orlacchio A, Bembi B, Cooper DN, Filocamo M, Beccari T.

Hum Mutat. 2009 Jun;30(6):978-84. doi: 10.1002/humu.20959.

PubMed [citation]

PMID:: 19370764

Mucolipidosis III Gamma.

Raas-Rothschild A, Spiegel R.

2010 Jan 28 [updated 2019 Nov 21]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]

PMID:: 20301784

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001589723.5

#	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. Loss-of-function variants in GNPTG are known to be pathogenic (PMID: 19370764, 20301784). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with GNPTG-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change creates a premature translational stop signal (p.Val30Glyfs*52) in the GNPTG gene. It is expected to result in an absent or disrupted protein product.

#	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: Feb 20, 2024

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