GK5

glycerol kinase 5, the group of Glycerol kinases

Basic information

Region (hg38): 3:142157527-142225592

Links

ENSG00000175066 ∙ NCBI:256356 ∙ ∙ HGNC:28635 ∙ Uniprot:Q6ZS86 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GK5 gene.

• not_specified (29 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GK5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001039547.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			24	5		29
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	24	5	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GK5	protein_coding	protein_coding	ENST00000392993	16	62036

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00634	0.994	125709	0	38	125747	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	175	264	0.663	0.0000122	3472
Missense in Polyphen		64	98.052	0.65271		1338
Synonymous	-0.121	90	88.5	1.02	0.00000418	960
Loss of Function	3.62	10	32.1	0.311	0.00000164	380

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000154
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000266	0.000255
Middle Eastern	0.000109	0.000109
South Asian	0.000143	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: CDP-diacylglycerol biosynthesis;glycerol degradation (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.451
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.44

Haploinsufficiency Scores

• pHI: 0.118
• hipred: Y
• hipred_score: 0.639
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.271

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gk5
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: glycerol metabolic process;triglyceride metabolic process;phosphorylation;glycerol catabolic process;glycerol-3-phosphate biosynthetic process
• Cellular component: cytoplasm;mitochondrion
• Molecular function: glycerol kinase activity;ATP binding