PRPF40B

pre-mRNA processing factor 40 homolog B

Basic information

Region (hg38): 12:49568218-49644666

Links

ENSG00000110844 ∙ NCBI:25766 ∙ ∙ HGNC:25031 ∙ Uniprot:Q6NWY9 ∙ 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 PRPF40B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPF40B 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				1		1
missense			87			87
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	87	1	0

Variants in PRPF40B

This is a list of pathogenic ClinVar variants found in the PRPF40B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-49587627-C-T		not specified	Uncertain significance (Apr 24, 2023)
12-49587661-G-A		not specified	Likely benign (Jul 16, 2021)
12-49587685-T-C		not specified	Uncertain significance (Nov 21, 2024)
12-49587690-A-G		not specified	Uncertain significance (Dec 02, 2024)
12-49587695-G-A			Benign (Oct 25, 2024)
12-49587731-C-G			Benign (Dec 09, 2024)
12-49587939-T-C			Benign (May 12, 2021)
12-49588449-C-T			Uncertain significance (Nov 23, 2021)
12-49588455-G-A			Benign (Jan 23, 2025)
12-49588459-C-T			Likely benign (Jan 13, 2025)
12-49588460-A-G			Likely benign (Jul 19, 2022)
12-49588481-C-T			Benign (Jul 31, 2024)
12-49588535-C-T			Likely benign (Dec 07, 2023)
12-49588536-G-A			Benign (Apr 29, 2024)
12-49588559-C-G		not specified	Likely benign (Nov 09, 2024)
12-49588577-G-A		not specified	Uncertain significance (Sep 26, 2024)
12-49588614-C-A			Uncertain significance (Nov 11, 2024)
12-49598742-G-A			Likely benign (Apr 08, 2022)
12-49598749-G-A			Uncertain significance (May 23, 2023)
12-49598760-G-C		not specified	Uncertain significance (Nov 09, 2023)
12-49598793-G-A			Uncertain significance (May 13, 2022)
12-49598799-TCTC-T			Uncertain significance (Oct 13, 2022)
12-49598825-G-A		not specified	Uncertain significance (Feb 06, 2023)
12-49598900-G-A		not specified	Uncertain significance (Feb 27, 2023)
12-49598909-G-A			Benign (Jan 15, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRPF40B	protein_coding	protein_coding	ENST00000548825	26	76449

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000369	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	466	536	0.870	0.0000340	5799
Missense in Polyphen		166	199.69	0.83128		2087
Synonymous	-0.599	204	193	1.05	0.0000107	1717
Loss of Function	5.89	7	53.5	0.131	0.00000266	613

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000343	0.000329
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.0000994	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in pre-mRNA splicing. {ECO:0000269|PubMed:9700202}.
• Pathway: Spliceosome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0828

Intolerance Scores

• rvis_EVS: -1.46
• rvis_percentile_EVS: 3.81

Haploinsufficiency Scores

• pHI: 0.469
• hipred: N
• hipred_score: 0.372
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.846

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prpf40b

Gene ontology

• Biological process: mRNA splicing, via spliceosome;mRNA cis splicing, via spliceosome
• Cellular component: U1 snRNP;nuclear speck;U2-type prespliceosome
• Molecular function: RNA binding