KHNYN

protein-coding

KH and NYN domain containing

Gene summary

The protein encoded by this gene contains a ribonuclease NYN domain and belongs to the N4BP1 family. The protein is a cofactor for the zinc finger antiviral protein (ZAP protein) which targets viral RNA for degradation and restricts SARS-CoV-2 infection. [provided by RefSeq, Sep 2021]

Previous symbols:

KIAA0323

MANE transcript

NM_015299.3

Inheritance

—

ClinVar variants

U:103B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr14:24,429,286-24,441,843

External References & Databases

Ensembl (ENSG00000100441)

Transcript & Mutation Effects

hg38 • Region Span ~12.6 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 KHNYN variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 98

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015299.3. 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				1 clinvar		1
missense			97 clinvar	2 clinvar		99
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	103	3	0	106

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015299.3	RefSeq	NP_056114.1	7	MANE Select
ENST00000553935.6	Ensembl	ENSP00000450799.1	7	MANE Select
NM_001290256.2	RefSeq	NP_001277185.1	8	Standard
NM_001290257.2	RefSeq	NP_001277186.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function
RNA binding

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000251343
Coding exons: 7
Length: 12049
Individuals with no LoFs: 125534
Homozygous LoFs: 3
Heterozygous LoFs: 211
Defined: 125748
p: 0.000851

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.347	385	405	0.951	0.0000231	4360
Missense (PolyPhen)		125	181.16	0.69		1854
Synonymous	0.388	154	160	0.961	0.00000850	1436
Loss of Function	2.02	17	28.6	0.594	0.00000155	291

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00058	0.00058	rare
Ashkenazi Jewish	0.013	0.013	notable
East Asian	0.00011	0.00011	rare
Finnish	0.00042	0.00042	rare
European (Non-Finnish)	0.00043	0.00041	rare
South Asian	0.000098	0.000098	rare
Other	0.00099	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0949

Intolerance Scores

LoFtool: 0.798
RVIS EVS: -0.82
RVIS percentile EVS: 11.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.776

Gene Damage Prediction

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