PRPF40A

pre-mRNA processing factor 40 homolog A, the group of Spliceosomal A complex

Basic information

Region (hg38): 2:152651593-152718012

Previous symbols: [ "FNBP3" ]

Links

ENSG00000196504

∙ NCBI:55660 ∙ OMIM:612941 ∙ HGNC:16463 ∙ Uniprot:O75400 ∙ 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 PRPF40A gene.

not_specified (58 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPF40A gene is commonly pathogenic or not. These statistics are base on transcript: NM_001365597.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			58 clinvar			58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	0	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRPF40A	protein_coding	protein_coding	ENST00000410080	26	66405

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0391	0.961	124621	0	17	124638	0.0000682

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.33	261	463	0.564	0.0000236	6128
Missense in Polyphen		14	36.443	0.38416		440
Synonymous	-2.52	181	143	1.27	0.00000703	1604
Loss of Function	5.10	14	54.7	0.256	0.00000291	738

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000946	0.0000936
Ashkenazi Jewish	0.000203	0.000199
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000109	0.000106
Middle Eastern	0.00	0.00
South Asian	0.0000341	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Binds to WASL/N-WASP and suppresses its translocation from the nucleus to the cytoplasm, thereby inhibiting its cytoplasmic function (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape and migration. May play a role in cytokinesis. May be involved in pre-mRNA splicing. {ECO:0000250, ECO:0000269|PubMed:21834987}.;
Pathway: Spliceosome - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in squamous cell - TarBase;mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec: 0.178

Intolerance Scores

loftool: 0.299
rvis_EVS: -1.11
rvis_percentile_EVS: 6.72

Haploinsufficiency Scores

pHI: 0.461
hipred: Y
hipred_score: 0.625
ghis: 0.699

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.922

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Prpf40a
Phenotype

Gene ontology

Biological process: mRNA splicing, via spliceosome;cytoskeleton organization;cell cycle;regulation of cell shape;cell migration;regulation of cytokinesis;mRNA cis splicing, via spliceosome;cell division
Cellular component: nucleoplasm;U1 snRNP;cytosol;membrane;nuclear matrix;nuclear speck;U2-type prespliceosome
Molecular function: RNA binding;protein binding