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.

• not_specified (40 variants)

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. These statistics are base on transcript: NM_000203370.2. 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			34	6		40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	6	0

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