PRPF38B

pre-mRNA processing factor 38B

Basic information

Region (hg38): 1:108692310-108702928

Links

ENSG00000134186 ∙ NCBI:55119 ∙ ∙ HGNC:25512 ∙ Uniprot:Q5VTL8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRPF38B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPF38B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			31		1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	0	1

Variants in PRPF38B

This is a list of pathogenic ClinVar variants found in the PRPF38B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-108692656-C-T		not specified	Uncertain significance (Jul 14, 2021)
1-108692685-G-A		not specified	Uncertain significance (Dec 14, 2024)
1-108692698-A-G		not specified	Uncertain significance (Sep 11, 2024)
1-108695711-G-A		not specified	Uncertain significance (Nov 11, 2024)
1-108695739-A-G		not specified	Uncertain significance (Feb 27, 2023)
1-108696296-G-A		not specified	Uncertain significance (Aug 13, 2021)
1-108698752-G-T		not specified	Uncertain significance (Mar 08, 2025)
1-108699199-A-G		not specified	Uncertain significance (Aug 02, 2023)
1-108699322-C-T		not specified	Uncertain significance (May 27, 2022)
1-108699323-G-A		not specified	Uncertain significance (Apr 01, 2024)
1-108699346-C-T		not specified	Uncertain significance (Dec 15, 2022)
1-108699381-A-T		not specified	Uncertain significance (Nov 03, 2023)
1-108699407-G-T		not specified	Uncertain significance (Aug 20, 2024)
1-108699434-G-A			Benign (Jan 11, 2019)
1-108699443-A-G		not specified	Uncertain significance (Apr 01, 2024)
1-108699445-A-G		not specified	Uncertain significance (May 26, 2023)
1-108699476-G-A		not specified	Uncertain significance (Feb 27, 2023)
1-108699482-G-A		not specified	Uncertain significance (Oct 03, 2022)
1-108699486-C-G		not specified	Uncertain significance (Jul 12, 2023)
1-108699487-T-A		not specified	Uncertain significance (May 11, 2022)
1-108699520-G-A		not specified	Uncertain significance (Mar 11, 2025)
1-108699524-G-C		not specified	Uncertain significance (Oct 07, 2024)
1-108699563-G-A		not specified	Uncertain significance (Oct 06, 2021)
1-108699701-G-A		High myopia • not specified	Uncertain significance (Sep 01, 2021)
1-108699745-T-C		not specified	Uncertain significance (Aug 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRPF38B	protein_coding	protein_coding	ENST00000370025	6	9481

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.702	0.298	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.92	223	320	0.697	0.0000184	3599
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000261	0.000261
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000722	0.0000703
Middle Eastern	0.000167	0.000163
South Asian	0.000328	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be required for pre-mRNA splicing. {ECO:0000305}.
• Pathway: Spliceosome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.238
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.613
• hipred: Y
• hipred_score: 0.625
• ghis: 0.609

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.841

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prpf38b
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: mRNA processing;RNA splicing
• Cellular component: spliceosomal complex;precatalytic spliceosome
• Molecular function: RNA binding