GALK2

galactokinase 2

Basic information

Region (hg38): 15:49155655-49367869

Links

ENSG00000156958 ∙ NCBI:2585 ∙ OMIM:137028 ∙ HGNC:4119 ∙ Uniprot:Q01415 ∙ 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 GALK2 gene.

• Inborn genetic diseases (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALK2 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in GALK2

This is a list of pathogenic ClinVar variants found in the GALK2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-49170348-G-A		not specified	Uncertain significance (Jan 19, 2024)
15-49170353-G-T		not specified	Uncertain significance (Feb 27, 2024)
15-49170356-C-G		not specified	Uncertain significance (Oct 26, 2022)
15-49201181-A-G		not specified	Uncertain significance (Feb 06, 2023)
15-49201245-T-A		not specified	Uncertain significance (Dec 28, 2022)
15-49217220-T-C		not specified	Uncertain significance (Jan 30, 2024)
15-49235888-A-C		not specified	Uncertain significance (Jan 06, 2023)
15-49235937-T-C		not specified	Uncertain significance (Aug 30, 2021)
15-49239225-A-T		not specified	Uncertain significance (Aug 28, 2023)
15-49239249-G-A		not specified	Uncertain significance (Feb 23, 2023)
15-49239251-A-G		not specified	Uncertain significance (May 24, 2023)
15-49239351-G-A		not specified	Uncertain significance (Mar 24, 2023)
15-49282048-T-A		not specified	Uncertain significance (Dec 02, 2022)
15-49282054-A-G		not specified	Uncertain significance (Feb 27, 2023)
15-49283602-G-A		not specified	Uncertain significance (Jan 10, 2023)
15-49283602-G-T		not specified	Uncertain significance (Feb 12, 2024)
15-49283704-C-T		not specified	Uncertain significance (Aug 04, 2023)
15-49283713-G-T		not specified	Uncertain significance (Feb 15, 2023)
15-49283714-C-G		not specified	Uncertain significance (Feb 15, 2023)
15-49292505-G-A		not specified	Uncertain significance (Aug 07, 2023)
15-49319628-G-A		not specified	Uncertain significance (Nov 19, 2022)
15-49319645-A-G		not specified	Uncertain significance (Feb 21, 2024)
15-49319648-G-A		not specified	Uncertain significance (Nov 09, 2021)
15-49319681-T-C		not specified	Uncertain significance (Jul 30, 2023)
15-49319751-G-A		not specified	Uncertain significance (Jun 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALK2	protein_coding	protein_coding	ENST00000560031	10	212214

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.90e-14	0.0671	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.395	270	252	1.07	0.0000128	2986
Missense in Polyphen		107	101.11	1.0583		1172
Synonymous	1.60	73	92.5	0.789	0.00000487	888
Loss of Function	0.575	22	25.1	0.876	0.00000150	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00140	0.00140
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000381	0.000378
Middle Eastern	0.000163	0.000163
South Asian	0.000196	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts on GalNAc. Also acts as a galactokinase when galactose is present at high concentrations. May be involved in a salvage pathway for the reutilization of free GalNAc derived from the degradation of complex carbohydrates. {ECO:0000269|PubMed:16006554}.
• Pathway: Galactose metabolism (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.153
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.208
• hipred: N
• hipred_score: 0.237
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.852

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galk2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;galactose catabolic process via UDP-galactose;carbohydrate phosphorylation
• Cellular component: cytoplasm;cytosol
• Molecular function: galactokinase activity;ATP binding;galactose binding;N-acetylgalactosamine kinase activity