PRPF4B

pre-mRNA processing factor 4B

Basic information

Region (hg38): 6:4021266-4064983

Links

ENSG00000112739 ∙ NCBI:8899 ∙ OMIM:602338 ∙ HGNC:17346 ∙ Uniprot:Q13523 ∙ 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 PRPF4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPF4B 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				3	2	5
missense			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	28	5	2

Variants in PRPF4B

This is a list of pathogenic ClinVar variants found in the PRPF4B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-4021433-C-T		not specified	Uncertain significance (Aug 15, 2023)
6-4021436-C-T		not specified	Uncertain significance (Oct 13, 2023)
6-4021453-C-T		not specified	Uncertain significance (Dec 20, 2023)
6-4031690-A-G		not specified	Uncertain significance (Jan 22, 2024)
6-4031721-A-G			Benign (Dec 14, 2017)
6-4031750-A-G		not specified	Uncertain significance (Jul 14, 2021)
6-4031892-G-A		not specified	Uncertain significance (Jun 30, 2022)
6-4032013-A-G		not specified	Likely benign (Apr 12, 2022)
6-4032035-T-C		not specified	Uncertain significance (May 23, 2023)
6-4032049-A-G		not specified	Uncertain significance (Jun 19, 2024)
6-4032065-G-A		not specified	Uncertain significance (May 23, 2023)
6-4032088-C-T		not specified	Uncertain significance (Jul 26, 2022)
6-4032311-T-C		not specified	Uncertain significance (Feb 23, 2023)
6-4032335-A-G		not specified	Uncertain significance (Apr 25, 2022)
6-4032430-A-G		not specified	Likely benign (Feb 05, 2024)
6-4032440-G-A		not specified	Uncertain significance (Feb 10, 2022)
6-4032547-A-G		not specified	Uncertain significance (Dec 19, 2023)
6-4032557-G-C		not specified	Uncertain significance (Mar 29, 2024)
6-4032560-G-A		not specified	Uncertain significance (Aug 12, 2021)
6-4032637-A-G		not specified	Uncertain significance (Mar 07, 2023)
6-4032667-C-T		not specified	Uncertain significance (Jun 29, 2023)
6-4032713-G-C		not specified	Uncertain significance (Nov 16, 2021)
6-4032740-G-A		not specified	Uncertain significance (Dec 18, 2023)
6-4037408-G-A		not specified	Uncertain significance (Aug 12, 2021)
6-4037429-G-A		not specified	Uncertain significance (May 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRPF4B	protein_coding	protein_coding	ENST00000337659	15	43717

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000245	125591	0	5	125596	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.59	314	551	0.570	0.0000300	6657
Missense in Polyphen		79	109.05	0.72444		1376
Synonymous	0.344	181	187	0.968	0.00000934	1855
Loss of Function	6.29	4	53.7	0.0744	0.00000392	611

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000472	0.0000472
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000291	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has a role in pre-mRNA splicing. Phosphorylates SF2/ASF.
• Pathway: mRNA Processing;TCR;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.0344
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.14

Haploinsufficiency Scores

• pHI: 0.908
• hipred: Y
• hipred_score: 0.816
• ghis: 0.666

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prpf4b

Gene ontology

• Biological process: mRNA splicing, via spliceosome;protein phosphorylation;RNA splicing
• Cellular component: nucleus;chromosome;nuclear speck;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding