rs193302853

Positions:

• chr16-1362561-GGTGGGCCTGGCTGGGAGCTGGGTGCTGCCCCTGC-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

The NM_032520.5(GNPTG):​c.609+28_610-16delGTGGGCCTGGCTGGGAGCTGGGTGCTGCCCCTGC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: GNPTG NM_032520.5 intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 0.957

Genes affected

GNPTG (HGNC:23026): (N-acetylglucosamine-1-phosphate transferase subunit gamma) This gene encodes the gamma sunbunit of the N-acetylglucosamine-1-phosphotransferase complex. This hexameric complex, composed of alpha, beta and gamma subunits, catalyzes the first step in synthesis of a mannose 6-phosphate lysosomal recognition marker. This enzyme complex is necessary for targeting of lysosomal hydrolases to the lysosome. Mutations in the gene encoding the gamma subunit have been associated with mucolipidosis IIIC, also known as mucolipidosis III gamma.[provided by RefSeq, Feb 2010]

GNPTG (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 16-1362561-GGTGGGCCTGGCTGGGAGCTGGGTGCTGCCCCTGC-G is Pathogenic according to our data. Variant chr16-1362561-GGTGGGCCTGGCTGGGAGCTGGGTGCTGCCCCTGC-G is described in ClinVar as [Pathogenic]. Clinvar id is 21719.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr16-1362561-GGTGGGCCTGGCTGGGAGCTGGGTGCTGCCCCTGC-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNPTG	NM_032520.5	c.609+28_610-16delGTGGGCCTGGCTGGGAGCTGGGTGCTGCCCCTGC		intron_variant		ENST00000204679.9	NP_115909.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNPTG	ENST00000204679.9	c.609+28_610-16delGTGGGCCTGGCTGGGAGCTGGGTGCTGCCCCTGC		intron_variant		1	NM_032520.5	ENSP00000204679.4

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

GNPTG-mucolipidosis Pathogenic:1

Pathogenic, no assertion criteria provided

curation

GeneReviews

Jul 05, 2012

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs193302853; hg19: chr16-1412562;