ZFR2

protein-coding

zinc finger RNA binding protein 2

Gene summary

Predicted to enable double-stranded RNA binding activity and single-stranded RNA binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KIAA1086

MANE transcript

NM_015174.2

Inheritance

—

ClinVar variants

U:226B:25

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr19:3,804,024-3,869,038

External References & Databases

Ensembl (ENSG00000105278)

Transcript & Mutation Effects

hg38 • Region Span ~65.0 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 ZFR2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 241

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015174.2. 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			3 clinvar	5 clinvar		8
missense			220 clinvar	20 clinvar		240
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	226	25	0	251

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015174.2	RefSeq	NP_055989.1	19	MANE Select
ENST00000262961.9	Ensembl	ENSP00000262961.3	19	MANE Select
NM_001145640.2	RefSeq	NP_001139112.1	2	Standard
ENST00000438164.2	Ensembl	ENSP00000388974.2	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

double-stranded RNA binding
single-stranded RNA binding
zinc ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262961
Coding exons: 19
Length: 65009
Individuals with no LoFs: 124579
Homozygous LoFs: 0
Heterozygous LoFs: 70
Defined: 124649
p: 0.000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.00888	552	551	1.00	0.0000378	5803
Missense (PolyPhen)		120	133.84	0.89662		1539
Synonymous	-0.359	264	257	1.03	0.0000202	1971
Loss of Function	0.158	39	40.1	0.973	0.00000202	470

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00053	0.00052	rare
Latino/Admixed American	0.00044	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00025	0.00022	rare
Finnish	0.00020	0.00019	rare
European (Non-Finnish)	0.00022	0.00021	rare
South Asian	0.00047	0.00042	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0918

Intolerance Scores

LoFtool: 0.783
RVIS EVS: 0.39
RVIS percentile EVS: 75.71

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.248

Gene Damage Prediction

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