GASK1A

golgi associated kinase 1A, the group of Golgi associated kinase family

Basic information

Region (hg38): 3:42979086-43067898

Previous symbols: [ "C3orf41", "FAM198A" ]

Links

ENSG00000144649 ∙ NCBI:729085 ∙ ∙ HGNC:24485 ∙ Uniprot:Q9UFP1 ∙ 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 GASK1A gene.

• Inborn genetic diseases (4 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GASK1A 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			4		1	5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	1

Variants in GASK1A

This is a list of pathogenic ClinVar variants found in the GASK1A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-43032279-C-T		not specified	Likely benign (Feb 27, 2024)
3-43032280-G-A		not specified	Uncertain significance (May 31, 2023)
3-43032291-C-T		not specified	Uncertain significance (Jun 11, 2021)
3-43032303-C-T		not specified	Uncertain significance (Mar 14, 2023)
3-43032342-G-A		not specified	Uncertain significance (Aug 22, 2023)
3-43032343-C-T		not specified	Likely benign (Feb 17, 2022)
3-43032381-G-A		not specified	Likely benign (Feb 03, 2022)
3-43032444-C-T		not specified	Uncertain significance (Jun 28, 2022)
3-43032445-G-A		not specified	Uncertain significance (Jan 16, 2024)
3-43032475-G-A		not specified	Uncertain significance (Mar 01, 2024)
3-43032879-G-C			Benign (Mar 19, 2018)
3-43032958-C-G		not specified	Uncertain significance (Oct 04, 2022)
3-43033021-C-G		not specified	Uncertain significance (Jan 24, 2024)
3-43033032-G-T		not specified	Uncertain significance (Mar 07, 2024)
3-43033065-A-T		not specified	Uncertain significance (Dec 13, 2022)
3-43033067-G-C		not specified	Uncertain significance (Oct 25, 2022)
3-43033230-C-A		not specified	Uncertain significance (Jan 19, 2024)
3-43033312-G-A		not specified	Uncertain significance (Oct 04, 2022)
3-43033318-A-G		not specified	Uncertain significance (May 25, 2022)
3-43033333-C-T		not specified	Uncertain significance (Jan 18, 2022)
3-43033335-T-C		not specified	Uncertain significance (Sep 15, 2021)
3-43033413-G-A		not specified	Uncertain significance (Sep 28, 2022)
3-43033498-C-T		not specified	Likely benign (Sep 06, 2022)
3-43033525-G-A		not specified	Uncertain significance (Apr 25, 2022)
3-43053527-G-A		not specified	Uncertain significance (Feb 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GASK1A	protein_coding	protein_coding	ENST00000430121	5	80945

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.75e-16	0.00379	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.00	234	337	0.693	0.0000197	3690
Missense in Polyphen		83	109.85	0.75558		1254
Synonymous	1.43	122	144	0.849	0.00000859	1238
Loss of Function	-0.494	22	19.6	1.12	0.00000101	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.64
• rvis_percentile_EVS: 96.11

Haploinsufficiency Scores

• pHI: 0.0624

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Fam198a