PRR3

protein-coding

proline rich 3, the group of Zinc fingers CCCH-type

Gene summary

Enables RNA binding activity. Predicted to be involved in positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled. Predicted to be part of PTW/PP1 phosphatase complex. Predicted to be active in chromatin. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_025263.4

Inheritance

—

ClinVar variants

U:29B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr6:30,557,280-30,563,723

External References & Databases

Ensembl (ENSG00000204576)

Transcript & Mutation Effects

hg38 • Region Span ~6.4 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 PRR3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 31

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025263.4. 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
missense			27 clinvar	5 clinvar		32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	29	5	0	34

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025263.4	RefSeq	NP_079539.2	4	MANE Select
ENST00000376560.8	Ensembl	ENSP00000365744.4	4	MANE Select
NM_001077497.3	RefSeq	NP_001070965.1	3	Standard
ENST00000376557.3	Ensembl	ENSP00000365740.3	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding
protein binding
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376560
Coding exons: 4
Length: 6838
Individuals with no LoFs: 124810
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 124821
p: 0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.782	88	111	0.791	0.00000578	1201
Missense (PolyPhen)		24	37.169	0.6457		447
Synonymous	-0.517	45	40.8	1.10	0.00000210	390
Loss of Function	1.35	6	10.8	0.557	6.86e-7	98

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00021	0.00019	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000046	0.000044	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.485
RVIS EVS: 0.06
RVIS percentile EVS: 58.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.297

Gene Damage Prediction

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