NM_032520.5(GNPTG):c.417_429del (p.Leu140fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 31, 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:: RCV001390867.5

Allele description [Variation Report for NM_032520.5(GNPTG):c.417_429del (p.Leu140fs)]

NM_032520.5(GNPTG):c.417_429del (p.Leu140fs)

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.417_429del (p.Leu140fs)

HGVS:

NC_000016.10:g.1362211_1362223del
NG_016985.1:g.15313_15325del
NG_033129.1:g.57487_57499del
NM_032520.5:c.417_429delMANE SELECT
NP_115909.1:p.Leu140fs
NC_000016.9:g.1412207_1412219del
NC_000016.9:g.1412212_1412224del

Protein change:

L140fs

Links:

dbSNP: rs2141862900

NCBI 1000 Genomes Browser:

rs2141862900

Molecular consequence:

NM_032520.5:c.417_429del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV001592733	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 31, 2022)	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

SCV001592733

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 31, 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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001592733.4

#	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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1076841). This variant has not been reported in the literature in individuals affected with GNPTG-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu140Lysfs*18) in the GNPTG gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GNPTG are known to be pathogenic (PMID: 19370764, 20301784).

#	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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