PRKRIP1

protein-coding

PRKR interacting protein 1

Gene summary

Predicted to enable double-stranded RNA binding activity; protein kinase binding activity; and protein kinase inhibitor activity. Involved in renal system process. Located in actin cytoskeleton and cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_024653.4

Inheritance

—

ClinVar variants

U:24B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.18

Max pathogenic AF

—

Genomic locus

chr7:102,363,872-102,426,676

External References & Databases

Ensembl (ENSG00000128563)

Transcript & Mutation Effects

hg38 • Region Span ~62.8 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 PRKRIP1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 24

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024653.4. 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						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 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024653.4	RefSeq	NP_078929.1	6	MANE Select
ENST00000397912.3	Ensembl	ENSP00000381010.3	6	MANE Select
ENST00000496391.5	Ensembl	ENSP00000419270.1	6	Standard
ENST00000496391.6	Ensembl	ENSP00000419270.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

renal system process
negative regulation of protein kinase activity
negative regulation of phosphorylation

Molecular Function

double-stranded RNA binding
protein kinase inhibitor activity
protein binding
protein kinase binding

Cellular Component

nucleolus
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000496391
Coding exons: 6
Length: 62805
Individuals with no LoFs: 125711
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125748
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.285	100	108	0.923	0.00000624	1189
Missense (PolyPhen)		17	28.762	0.59105		293
Synonymous	-0.540	43	38.7	1.11	0.00000214	331
Loss of Function	-0.608	15	12.7	1.18	7.72e-7	134

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00018	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00023	0.00023	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds double-stranded RNA. Inhibits EIF2AK2 kinase activity (By similarity). {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.747
RVIS EVS: 0.17
RVIS percentile EVS: 65.56

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.706

Gene Damage Prediction

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