PRPF40A

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

Basic information

Region (hg38): 2:152651592-152718012

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.

• Inborn genetic diseases (13 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.

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			13			13
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	13	0	1

Variants in PRPF40A

This is a list of pathogenic ClinVar variants found in the PRPF40A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-152657983-T-C		not specified	Uncertain significance (Jul 27, 2021)
2-152659162-G-T		not specified	Uncertain significance (Oct 12, 2022)
2-152659277-G-A		not specified	Uncertain significance (Oct 14, 2023)
2-152664205-T-C			Benign (Jan 30, 2018)
2-152669254-A-T		not specified	Uncertain significance (Jan 06, 2023)
2-152669267-A-G		not specified	Uncertain significance (Nov 16, 2021)
2-152670383-TATAGCA-T			Benign (Jan 30, 2018)
2-152671338-T-C		not specified	Uncertain significance (Mar 13, 2023)
2-152672537-G-A		not specified	Uncertain significance (Jun 03, 2022)
2-152676556-T-C		not specified	Uncertain significance (Oct 26, 2021)
2-152676645-G-C		not specified	Uncertain significance (Jun 30, 2023)
2-152676669-G-A		not specified	Uncertain significance (Mar 04, 2024)
2-152676672-G-C		not specified	Uncertain significance (Nov 28, 2023)
2-152676725-A-C		not specified	Uncertain significance (Dec 03, 2021)
2-152679382-C-T		not specified	Uncertain significance (Oct 04, 2022)
2-152693053-T-C		not specified	Uncertain significance (Nov 10, 2022)
2-152717384-C-A		not specified	Uncertain significance (Oct 03, 2023)
2-152717418-G-A		not specified	Uncertain significance (Jan 19, 2024)
2-152717421-G-C		not specified	Uncertain significance (Jan 31, 2024)
2-152717424-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-152717427-T-G		not specified	Uncertain significance (Mar 06, 2023)

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

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