IFNK

protein-coding

interferon kappa, the group of Interferons

Gene summary

This gene encodes a member of the type I interferon family. Type I interferons are a group of related glycoproteins that play an important role in host defenses against viral infections. This protein is expressed in keratinocytes and the gene is found on chromosome 9, adjacent to the type I interferon cluster. [provided by RefSeq, Jul 2008]

MANE transcript

NM_020124.3

Inheritance

—

ClinVar variants

U:24B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.37

Max pathogenic AF

—

Genomic locus

chr9:27,524,290-27,526,498

External References & Databases

Ensembl (ENSG00000147896)

Transcript & Mutation Effects

hg38 • Region Span ~2.2 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 IFNK variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 25

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020124.3. 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						0
missense			24 clinvar	1 clinvar		25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	24	1	0	25

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020124.3	RefSeq	NP_064509.2	1	MANE Select
ENST00000276943.3	Ensembl	ENSP00000276943.2	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Jak-STAT signaling pathway - Homo sapiens (human)
Cytokine-cytokine receptor interaction - Homo sapiens (human)
RIG-I-like receptor signaling pathway - Homo sapiens (human)
JAK-STAT-Core
RIG-I-like Receptor Signaling

Biological Process

adaptive immune response
T cell activation involved in immune response
natural killer cell activation involved in immune response
regulation of transcription, DNA-templated
humoral immune response

Molecular Function

cytokine activity
type I interferon receptor binding

Cellular Component

extracellular region
extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000276943
Coding exons: 1
Length: 2185
Individuals with no LoFs: 118814
Homozygous LoFs: 148
Heterozygous LoFs: 6783
Defined: 125745
p: 0.0279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.341	112	102	1.09	0.00000461	1397
Missense (PolyPhen)		36	23.976	1.5015		363
Synonymous	-0.194	39	37.5	1.04	0.00000174	348
Loss of Function	-1.01	12	8.77	1.37	5.57e-7	100

Population LoF Frequency

Population	CAF	p-value	Status
African	0.043	0.043	notable
Latino/Admixed American	0.012	0.012	notable
Ashkenazi Jewish	0.0092	0.0091	notable
East Asian	0.0014	0.0014	notable
Finnish	0.039	0.038	notable
European (Non-Finnish)	0.031	0.030	notable
South Asian	0.044	0.044	notable
Other	0.028	0.028	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in the regulation of immune cell function. Cytokine that imparts cellular protection against viral infection in a species-specific manner. Activates the interferon- stimulated response element signaling pathway. It is able to directly modulate cytokine release from monocytes and dendritic cells. Binds heparin. {ECO:0000269|PubMed:11514542, ECO:0000269|PubMed:12391192}.;

Recessive Scores

pRec: 0.183

Intolerance Scores

LoFtool: 0.862
RVIS EVS: 0.46
RVIS percentile EVS: 78.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.694

Gene Damage Prediction

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