NM_001205019.2:c.1255C>T

Variant names:

• chrX-30720639-C-T
• rs132630329
• NM_001205019.2:c.1255C>T

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_001205019.2(GK):​c.1255C>T​(p.Arg419*) variant causes a stop gained change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 23)
• Consequence: GK NM_001205019.2 stop_gained
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 4.01
• Publications: 2 publications found

Genes affected

GK (HGNC:4289): (glycerol kinase) The protein encoded by this gene belongs to the FGGY kinase family. This protein is a key enzyme in the regulation of glycerol uptake and metabolism. It catalyzes the phosphorylation of glycerol by ATP, yielding ADP and glycerol-3-phosphate. Mutations in this gene are associated with glycerol kinase deficiency (GKD). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]

GK-AS1 (HGNC:40255): (GK antisense RNA 1)

ENSG00000241886 (HGNC:):

ACMG classification

Our verdict: Pathogenic. The variant received 11 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-30720639-C-T is Pathogenic according to our data. Variant chrX-30720639-C-T is described in ClinVar as Pathogenic. ClinVar VariationId is 10945.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001205019.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GK	NM_001205019.2	MANE Select	c.1255C>T	p.Arg419*	stop_gained	Exon 17 of 21	NP_001191948.1
	GK	NM_001437590.1		c.1321C>T	p.Arg441*	stop_gained	Exon 17 of 21	NP_001424519.1
	GK	NM_001128127.3		c.1237C>T	p.Arg413*	stop_gained	Exon 16 of 20	NP_001121599.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GK	ENST00000427190.6	TSL:5 MANE Select	c.1255C>T	p.Arg419*	stop_gained	Exon 17 of 21	ENSP00000401720.2
	GK	ENST00000378943.7	TSL:1	c.1237C>T	p.Arg413*	stop_gained	Exon 16 of 20	ENSP00000368226.3
	GK	ENST00000378946.7	TSL:1	c.1255C>T	p.Arg419*	stop_gained	Exon 17 of 20	ENSP00000368229.3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 23

Alfa AF: 0.0000769 Hom.: 1

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Inborn glycerol kinase deficiency Pathogenic:1

Aug 01, 1998

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.74	D
BayesDel_noAF	Pathogenic	0.63
CADD	Pathogenic	40
DANN	Uncertain	1.0
FATHMM_MKL	Uncertain	0.93	D
PhyloP100		4.0
Vest4		0.88
GERP RS		4.6
PromoterAI		-0.0051	Neutral
Mutation Taster		=1/199	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.34		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.32		Position offset: 23
DS_AL_spliceai		0.34		Position offset: -18

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

Other links and lift over

dbSNP: rs132630329; hg19: chrX-30738756;