IK

protein-coding

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

Gene summary

The protein encoded by this gene was identified by its RED repeat, a stretch of repeated arginine, glutamic acid and aspartic acid residues. The protein localizes to discrete dots within the nucleus, excluding the nucleolus. Its function is unknown. This gene maps to chromosome 5; however, a pseudogene may exist on chromosome 2. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006083.4

Inheritance

—

ClinVar variants

U:51B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr5:140,647,058-140,662,480

External References & Databases

Ensembl (ENSG00000113141)

Transcript & Mutation Effects

hg38 • Region Span ~15.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IK variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006083.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		1 clinvar	2
missense			39 clinvar	2 clinvar		41
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	51	2	1	54

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006083.4	RefSeq	NP_006074.2	20	MANE Select
ENST00000417647.7	Ensembl	ENSP00000396301.2	20	MANE Select
ENST00000502899.2	Ensembl	ENSP00000426764.2	8	Standard
ENST00000503332.5	Ensembl	ENSP00000421930.1	4	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ik	Danio rerio	Structure: pericardium Quality: edematous abnormal

Gene / Model

Organism

Observed Phenotype

Danio rerio

Structure: pericardium

Quality: edematous

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mitotic cell cycle
mRNA splicing, via spliceosome
mitotic spindle assembly checkpoint
viral process
protein localization to kinetochore

Molecular Function

protein binding
identical protein binding

Cellular Component

nuclear chromosome
nucleus
nucleoplasm
cytoplasm
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000417647
Coding exons: 20
Length: 15422
Individuals with no LoFs: 124802
Homozygous LoFs: 0
Heterozygous LoFs: 53
Defined: 124855
p: 0.000212

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.50	148	326	0.454	0.0000195	3695
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00047	0.00045	rare
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00017	rare
Finnish	0.000098	0.000093	rare
European (Non-Finnish)	0.00023	0.00021	rare
South Asian	0.00028	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.659

Gene Damage Prediction

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