INKA1

inka box actin regulator 1

Basic information

Region (hg38): 3:49803261-49805030

Previous symbols: [ "C3orf54", "FAM212A" ]

Links

ENSG00000185614 ∙ NCBI:389119 ∙ ∙ HGNC:32480 ∙ Uniprot:Q96EL1 ∙ 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 INKA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INKA1 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	3		23
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	3	0

Variants in INKA1

This is a list of pathogenic ClinVar variants found in the INKA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-49804184-T-G		not specified	Uncertain significance (May 31, 2022)
3-49804291-G-C		not specified	Uncertain significance (Apr 15, 2024)
3-49804334-G-A		not specified	Uncertain significance (Nov 26, 2024)
3-49804356-A-G		not specified	Likely benign (Dec 14, 2021)
3-49804367-G-T		not specified	Uncertain significance (Jan 01, 2025)
3-49804376-G-A		not specified	Uncertain significance (Feb 17, 2024)
3-49804379-G-T		not specified	Uncertain significance (May 28, 2024)
3-49804442-C-G		not specified	Uncertain significance (Feb 06, 2024)
3-49804443-G-T		not specified	Uncertain significance (Mar 28, 2024)
3-49804470-G-A		not specified	Likely benign (Feb 21, 2024)
3-49804506-G-A		not specified	Uncertain significance (Jun 17, 2024)
3-49804538-A-G		not specified	Likely benign (Nov 18, 2022)
3-49804556-G-A		not specified	Uncertain significance (Feb 07, 2025)
3-49804571-C-A		not specified	Uncertain significance (Feb 05, 2025)
3-49804577-C-T		not specified	Uncertain significance (Mar 24, 2023)
3-49804670-C-T		not specified	Uncertain significance (Sep 30, 2024)
3-49804711-G-C		not specified	Uncertain significance (Aug 05, 2024)
3-49804760-G-A		not specified	Uncertain significance (Jan 08, 2024)
3-49804784-C-T		not specified	Uncertain significance (Feb 22, 2025)
3-49804824-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-49804826-C-T		not specified	Uncertain significance (Apr 05, 2024)
3-49804848-G-A		not specified	Uncertain significance (Dec 04, 2024)
3-49804919-C-T		not specified	Uncertain significance (Mar 26, 2024)
3-49804934-A-G		not specified	Uncertain significance (Jul 16, 2024)
3-49804943-C-T		not specified	Uncertain significance (Feb 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INKA1	protein_coding	protein_coding	ENST00000333323	2	1777

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000614	0.741	125603	0	134	125737	0.000533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.799	143	173	0.829	0.0000114	1822
Missense in Polyphen		53	69.361	0.76411		705
Synonymous	0.619	57	63.3	0.901	0.00000324	624
Loss of Function	0.936	6	9.03	0.664	4.76e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00519	0.00517
Ashkenazi Jewish	0.00	0.00
East Asian	0.00179	0.00180
Finnish	0.00	0.00
European (Non-Finnish)	0.0000711	0.0000703
Middle Eastern	0.00179	0.00180
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of the serine/threonine-protein kinase PAK4 (PubMed:26607847). Acts by binding PAK4 in a substrate-like manner, inhibiting the protein kinase activity (PubMed:26607847). {ECO:0000269|PubMed:26607847}.

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.208
• ghis: 0.519

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Inka1
• Phenotype: reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: inka1a
• Affected structure: neurocranium
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: neural tube development;negative regulation of protein serine/threonine kinase activity
• Cellular component: nucleus;cytoplasm
• Molecular function: protein binding;protein kinase binding;protein serine/threonine kinase inhibitor activity