PRPF38A

pre-mRNA processing factor 38A, the group of Spliceosomal B complex

Basic information

Region (hg38): 1:52404602-52420836

Links

ENSG00000134748 ∙ NCBI:84950 ∙ OMIM:617031 ∙ HGNC:25930 ∙ Uniprot:Q8NAV1 ∙ 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 PRPF38A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPF38A 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in PRPF38A

This is a list of pathogenic ClinVar variants found in the PRPF38A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-52411178-A-C		not specified	Uncertain significance (Aug 04, 2023)
1-52411180-A-C		not specified	Uncertain significance (Feb 28, 2023)
1-52413909-C-T		not specified	Uncertain significance (Mar 23, 2023)
1-52413910-G-A		not specified	Uncertain significance (Nov 07, 2022)
1-52413939-C-G		not specified	Uncertain significance (Jan 24, 2024)
1-52413942-C-T		not specified	Uncertain significance (Oct 24, 2023)
1-52413955-T-C		not specified	Uncertain significance (Jan 03, 2024)
1-52414776-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-52414809-A-G		not specified	Uncertain significance (Jun 29, 2023)
1-52414811-C-T		not specified	Uncertain significance (May 31, 2023)
1-52415362-G-A		not specified	Uncertain significance (Oct 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRPF38A	protein_coding	protein_coding	ENST00000257181	10	16276

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.772	0.228	125734	0	10	125744	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.11	114	197	0.577	0.0000123	2050
Missense in Polyphen		26	61.203	0.42482		766
Synonymous	0.192	61	62.9	0.969	0.00000305	574
Loss of Function	3.61	4	22.5	0.178	0.00000151	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing as a component of the spliceosome. {ECO:0000269|PubMed:26673105, ECO:0000269|PubMed:28781166}.
• Pathway: Spliceosome - Homo sapiens (human);MECP2 and Associated Rett Syndrome;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.275
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.0439
• hipred: Y
• hipred_score: 0.816
• ghis: 0.702

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prpf38a

Gene ontology

• Biological process: mRNA splicing, via spliceosome
• Cellular component: nucleus;nucleoplasm;nuclear membrane;U2-type precatalytic spliceosome;precatalytic spliceosome
• Molecular function: RNA binding;protein binding