PRPF38B

protein-coding

pre-mRNA processing factor 38B

Gene summary

Enables RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleus. Predicted to be part of precatalytic spliceosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018061.4

Inheritance

—

ClinVar variants

U:66B:1

Top phenotype

High myopia

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr1:108,692,310-108,702,928

External References & Databases

Ensembl (ENSG00000134186)

Transcript & Mutation Effects

hg38 • Region Span ~10.6 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 PRPF38B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 61

not providedTotal: 2

High myopiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018061.4. 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			62 clinvar		1 clinvar	63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	66	0	1	67

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018061.4	RefSeq	NP_060531.2	6	MANE Select
ENST00000370025.9	Ensembl	ENSP00000359042.4	6	MANE Select
NM_001349757.2	RefSeq	NP_001336686.1	5	Standard
NM_001349758.2	RefSeq	NP_001336687.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)

Biological Process

mRNA processing
RNA splicing

Molecular Function

RNA binding

Cellular Component

spliceosomal complex
precatalytic spliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370025
Coding exons: 6
Length: 9481
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125748
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.92	223	320	0.697	0.0000184	3599
Missense (PolyPhen)		8	74.586	0.10726		874
Synonymous	0.653	98	107	0.919	0.00000500	1000
Loss of Function	4.36	7	34.7	0.202	0.00000288	311

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00026	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000072	0.000070	rare
South Asian	0.00033	0.00033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be required for pre-mRNA splicing. {ECO:0000305}.;

Recessive Scores

pRec: 0.100

Intolerance Scores

LoFtool: 0.238
RVIS EVS: 0.08
RVIS percentile EVS: 60.31

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.841

Gene Damage Prediction

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