PRPF39

protein-coding

pre-mRNA processing factor 39, the group of Small nucleolar RNA protein coding host genes

Gene summary

Predicted to contribute to pre-mRNA 5'-splice site binding activity. Predicted to be involved in mRNA 5'-splice site recognition. Predicted to be part of U1 snRNP; U2-type prespliceosome; and commitment complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_017922.4

Inheritance

—

ClinVar variants

U:63B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr14:45,084,107-45,116,282

External References & Databases

Ensembl (ENSG00000185246)

Transcript & Mutation Effects

hg38 • Region Span ~32.2 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 PRPF39 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 56

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017922.4. 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			61 clinvar	1 clinvar		62
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	63	1	0	64

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 49 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017922.4	RefSeq	NP_060392.3	13	MANE Select
ENST00000355765.11	Ensembl	ENSP00000348010.6	13	MANE Select
ENST00000424478.5	Ensembl	ENSP00000390867.1	3	Standard
ENST00000553605.1	Ensembl	ENSP00000452428.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mRNA 5'-splice site recognition

Molecular Function

pre-mRNA 5'-splice site binding

Cellular Component

commitment complex
U1 snRNP
U2-type prespliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355765
Coding exons: 13
Length: 32184
Individuals with no LoFs: 125565
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125570
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.69	192	329	0.583	0.0000158	4443
Missense (PolyPhen)		24	66.537	0.3607		905
Synonymous	-0.109	111	110	1.01	0.00000541	1147
Loss of Function	4.81	3	32.6	0.0919	0.00000157	453

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000072	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000068	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in pre-mRNA splicing. {ECO:0000250}.;

Recessive Scores

pRec: 0.0861

Intolerance Scores

LoFtool: 0.319
RVIS EVS: 0.15
RVIS percentile EVS: 64.51

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.854

Gene Damage Prediction

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