INKA2

inka box actin regulator 2

Basic information

Region (hg38): 1:111680629-111755824

Previous symbols: [ "C1orf183", "FAM212B" ]

Links

ENSG00000197852 ∙ NCBI:55924 ∙ ∙ HGNC:28045 ∙ Uniprot:Q9NTI7 ∙ 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 INKA2 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INKA2 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in INKA2

This is a list of pathogenic ClinVar variants found in the INKA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-111691119-T-C			Benign (May 14, 2021)
1-111691176-G-A			Benign (May 17, 2021)
1-111691365-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-111691446-T-A			Benign (Nov 12, 2018)
1-111691462-G-T			Benign (May 15, 2021)
1-111691593-C-T			Benign (May 17, 2021)
1-111695209-A-ATAATAT			Benign (May 14, 2021)
1-111695293-A-T			Benign (May 15, 2021)
1-111695324-CT-C		RAP1A-related disorder	Likely benign (Feb 17, 2020)
1-111695332-T-C			Likely benign (Nov 03, 2017)
1-111695352-T-C			Likely benign (May 03, 2018)
1-111695594-A-G			Benign (May 16, 2021)
1-111697229-C-T			Benign (May 15, 2021)
1-111697416-C-CT			Benign (Jun 02, 2021)
1-111697430-TG-T			Likely benign (Feb 05, 2018)
1-111697431-G-T			Likely benign (Dec 31, 2019)
1-111697432-C-G			Likely benign (May 29, 2018)
1-111697452-C-T			Likely benign (Jul 26, 2018)
1-111697503-G-A			Benign (Dec 31, 2019)
1-111703469-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-111704148-AT-A			Benign (May 14, 2021)
1-111704148-A-AT			Benign (Jun 04, 2021)
1-111704349-A-G		not specified	Uncertain significance (Jun 10, 2022)
1-111704434-G-A		not specified	Uncertain significance (Oct 12, 2022)
1-111704444-C-A			Likely benign (Jul 31, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INKA2	protein_coding	protein_coding	ENST00000357260	2	75195

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00799	0.935	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.345	168	181	0.928	0.0000104	1920
Missense in Polyphen		48	69.454	0.69111		750
Synonymous	-1.28	80	66.7	1.20	0.00000343	619
Loss of Function	1.65	5	10.9	0.460	7.01e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000163	0.000163
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of the serine/threonine-protein kinase PAK4. Acts by binding PAK4 in a substrate-like manner, inhibiting the protein kinase activity. {ECO:0000250|UniProtKB:Q96EL1}.

Intolerance Scores

• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.0983
• hipred: N
• hipred_score: 0.170
• ghis: 0.565

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Inka2
• Phenotype: skeleton phenotype; limbs/digits/tail phenotype

Gene ontology

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