IK

IK cytokine, the group of MicroRNA protein coding host genes|Spliceosomal B complex

Basic information

Region (hg38): 5:140647057-140662480

Links

ENSG00000113141 ∙ NCBI:3550 ∙ OMIM:600549 ∙ HGNC:5958 ∙ Uniprot:Q13123 ∙ 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 IK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IK 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					1	1
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				8	6	14
Total	0	0	12	8	7

Variants in IK

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

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

Position	Type	Phenotype	Significance	ClinVar
5-140647238-C-T			Benign (Dec 12, 2023)
5-140647251-C-T		Mitochondrial complex 1 deficiency, nuclear type 13	Pathogenic (Jun 01, 2008)
5-140647263-G-A			Likely benign (Jan 26, 2022)
5-140647264-GC-G		not specified	Uncertain significance (Dec 13, 2016)
5-140647265-C-A		Mitochondrial complex 1 deficiency, nuclear type 13	Uncertain significance (Jun 11, 2021)
5-140647273-T-C		Mitochondrial complex I deficiency, nuclear type 1	Uncertain significance (Jan 04, 2022)
5-140647274-T-C			Uncertain significance (Aug 12, 2022)
5-140647285-T-G		Inborn genetic diseases	Uncertain significance (Jun 30, 2023)
5-140647287-G-A		Mitochondrial complex I deficiency, nuclear type 1	Uncertain significance (Jan 12, 2018)
5-140647288-G-A			Uncertain significance (Apr 15, 2022)
5-140647294-T-G		Mitochondrial complex 1 deficiency, nuclear type 13	Pathogenic (Sep 17, 2020)
5-140647296-G-A			Likely benign (Aug 31, 2017)
5-140647309-G-T			Uncertain significance (Aug 08, 2022)
5-140647314-G-A			Likely benign (Jul 02, 2022)
5-140647320-A-T		Inborn genetic diseases	Uncertain significance (Jun 30, 2023)
5-140647324-G-A			Uncertain significance (Dec 22, 2022)
5-140647329-C-T		Mitochondrial complex I deficiency, nuclear type 1	Uncertain significance (Jan 12, 2018)
5-140647330-T-G		Cystic Leukoencephalopathy • Mitochondrial complex 1 deficiency, nuclear type 13	Pathogenic (-)
5-140647335-C-T		not specified • NDUFA2-related disorder	Benign (Jan 15, 2024)
5-140647373-G-C			Likely benign (Oct 13, 2023)
5-140647373-GGA-G			Likely benign (Aug 16, 2022)
5-140647376-G-A			Benign (Nov 15, 2022)
5-140647456-C-T			Likely benign (Apr 16, 2019)
5-140647471-G-C			Likely benign (Dec 11, 2023)
5-140647504-G-C			Uncertain significance (Jul 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IK	protein_coding	protein_coding	ENST00000417647	20	15422

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000249	1.00	124802	0	53	124855	0.000212

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.50	148	326	0.454	0.0000195	3695
Missense in Polyphen		33	129.52	0.25479		1464
Synonymous	1.02	90	103	0.872	0.00000517	952
Loss of Function	3.58	17	42.0	0.405	0.00000281	460

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000741	0.000719
Ashkenazi Jewish	0.00	0.00
East Asian	0.000174	0.000165
Finnish	0.0000978	0.0000928
European (Non-Finnish)	0.000226	0.000212
Middle Eastern	0.000174	0.000165
South Asian	0.000282	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing as a component of the spliceosome (PubMed:28781166). Auxiliary spliceosomal protein that regulates selection of alternative splice sites in a small set of target pre-mRNA species (Probable). Required for normal mitotic cell cycle progression (PubMed:22351768, PubMed:24252166). Recruits MAD1L1 and MAD2L1 to kinetochores, and is required to trigger the spindle assembly checkpoint (PubMed:22351768). Required for normal accumulation of SMU1 (PubMed:24945353). {ECO:0000269|PubMed:22351768, ECO:0000269|PubMed:24252166, ECO:0000269|PubMed:24945353, ECO:0000269|PubMed:28781166, ECO:0000305}.

Intolerance Scores

• loftool: 0.505
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.516
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.659

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ik

Zebrafish Information Network

• Gene name: ik
• Affected structure: pericardium
• Phenotype tag: abnormal
• Phenotype quality: edematous

Gene ontology

• Biological process: mitotic cell cycle;mRNA splicing, via spliceosome;mitotic spindle assembly checkpoint;viral process;protein localization to kinetochore
• Cellular component: nuclear chromosome;nucleus;nucleoplasm;cytoplasm;nuclear speck;U2-type precatalytic spliceosome;mitotic spindle pole
• Molecular function: protein binding;identical protein binding