GKAP1

G kinase anchoring protein 1

Basic information

Region (hg38): 9:83739425-83829516

Links

ENSG00000165113 ∙ NCBI:80318 ∙ OMIM:611356 ∙ HGNC:17496 ∙ Uniprot:Q5VSY0 ∙ 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 GKAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GKAP1 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in GKAP1

This is a list of pathogenic ClinVar variants found in the GKAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-83741959-T-C		not specified	Uncertain significance (Jun 01, 2023)
9-83742535-T-G		not specified	Uncertain significance (Dec 12, 2023)
9-83748356-A-G		not specified	Uncertain significance (Nov 30, 2021)
9-83768822-T-C		not specified	Uncertain significance (Oct 02, 2023)
9-83768828-T-A		not specified	Uncertain significance (Oct 27, 2022)
9-83768855-T-A		not specified	Uncertain significance (Jul 13, 2021)
9-83768895-G-A		not specified	Uncertain significance (Feb 02, 2022)
9-83768906-A-T		not specified	Uncertain significance (Jan 20, 2023)
9-83768925-T-G		not specified	Uncertain significance (Jun 29, 2023)
9-83780393-T-C		not specified	Uncertain significance (Mar 23, 2022)
9-83780397-A-C		not specified	Uncertain significance (Dec 15, 2023)
9-83784723-T-C		not specified	Uncertain significance (Apr 24, 2023)
9-83784758-T-A		not specified	Uncertain significance (Mar 01, 2024)
9-83799237-T-C		not specified	Uncertain significance (Aug 01, 2022)
9-83799256-G-C		not specified	Uncertain significance (Sep 16, 2021)
9-83799271-C-T		not specified	Uncertain significance (Jun 29, 2023)
9-83806366-G-A		not specified	Uncertain significance (Jan 19, 2024)
9-83806367-T-C		not specified	Uncertain significance (Apr 28, 2022)
9-83806370-T-A		not specified	Uncertain significance (Jan 17, 2023)
9-83806493-C-G		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GKAP1	protein_coding	protein_coding	ENST00000376371	11	90096

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0611	0.939	125694	0	24	125718	0.0000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.731	146	173	0.844	0.00000796	2397
Missense in Polyphen		38	57.17	0.66469		819
Synonymous	-0.488	67	62.1	1.08	0.00000302	633
Loss of Function	3.35	7	25.1	0.279	0.00000132	311

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000375	0.0000375
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000719	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.000427	0.000425
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates insulin-dependent IRS1 tyrosine phosphorylation in adipocytes by modulating the availability of IRS1 to IR tyrosine kinase. Its association with IRS1 is required for insulin-induced translocation of SLC2A4 to the cell membrane. Involved in TNF-induced impairment of insulin-dependent IRS1 tyrosine phosphorylation. {ECO:0000250|UniProtKB:Q9JMB0}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.188
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.324
• hipred: Y
• hipred_score: 0.528
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gkap1

Gene ontology

• Biological process: signal transduction;positive regulation of insulin receptor signaling pathway
• Cellular component: Golgi apparatus
• Molecular function: protein binding;identical protein binding