PRPF40B

protein-coding

pre-mRNA processing factor 40 homolog B

Gene summary

This gene encodes a WW-domain containing protein similar to yeast splicing factor PRP40. This protein has been shown to interact with Huntingtin and methyl CpG binding protein 2 (MeCP2). Alternative splicing results in different transcript variants. [provided by RefSeq, Aug 2014]

MANE transcript

NM_001031698.3

Inheritance

—

ClinVar variants

U:167B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr12:49,568,218-49,644,666

External References & Databases

Ensembl (ENSG00000110844)

Transcript & Mutation Effects

hg38 • Region Span ~76.4 kb

Loading mutation effect viewer...

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 PRPF40B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 155

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001031698.3. 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			3 clinvar	1 clinvar		4
missense			158 clinvar			158
nonsense			1 clinvar			1
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	167	1	0	168

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 64 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001031698.3	RefSeq	NP_001026868.2	26	MANE Select
ENST00000548825.7	Ensembl	ENSP00000448073.2	26	MANE Select
NM_001363607.2	RefSeq	NP_001350536.2	26	Standard
NM_001379030.1	RefSeq	NP_001365959.1	26	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)

Biological Process

mRNA splicing, via spliceosome
mRNA cis splicing, via spliceosome

Molecular Function

RNA binding

Cellular Component

U1 snRNP
nuclear speck
U2-type prespliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000548825
Coding exons: 26
Length: 76449
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125748
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.07	466	536	0.870	0.0000340	5799
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00018	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000099	0.000088	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in pre-mRNA splicing. {ECO:0000269|PubMed:9700202}.;

Recessive Scores

pRec: 0.0828

Intolerance Scores

RVIS EVS: -1.46
RVIS percentile EVS: 3.81

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.846

Gene Damage Prediction

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