PRPF18

pre-mRNA processing factor 18, the group of Spliceosomal C complex

Basic information

Region (hg38): 10:13586939-13668445

Links

ENSG00000165630 ∙ NCBI:8559 ∙ OMIM:604993 ∙ HGNC:17351 ∙ Uniprot:Q99633 ∙ 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 PRPF18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPF18 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in PRPF18

This is a list of pathogenic ClinVar variants found in the PRPF18 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-13597462-A-G		not specified	Uncertain significance (Sep 14, 2023)
10-13597509-G-A		not specified	Uncertain significance (Oct 05, 2022)
10-13600332-C-T		not specified	Uncertain significance (Jan 09, 2024)
10-13610151-T-C		not specified	Uncertain significance (Dec 17, 2021)
10-13611616-C-T		not specified	Uncertain significance (Jan 26, 2023)
10-13611673-A-G		not specified	Uncertain significance (Aug 18, 2023)
10-13613753-G-A		not specified	Uncertain significance (Apr 18, 2023)
10-13614042-A-G		not specified	Uncertain significance (Jul 05, 2022)
10-13630290-A-G		not specified	Uncertain significance (Oct 06, 2022)
10-13630329-A-G		not specified	Uncertain significance (May 03, 2023)
10-13651897-C-T		FRMD4A-related disorder	Likely benign (Apr 02, 2020)
10-13651898-G-A			Likely benign (-)
10-13651947-C-AGAATG		Severe intellectual disability-corpus callosum agenesis-facial dysmorphism-cerebellar ataxia syndrome	Likely pathogenic (Mar 14, 2024)
10-13651960-T-A		FRMD4A-related disorder	Benign (Dec 31, 2019)
10-13654453-G-A		not specified	Uncertain significance (Feb 28, 2023)
10-13654467-A-G		not specified	Uncertain significance (Dec 15, 2023)
10-13654482-G-A		not specified	Uncertain significance (Jun 02, 2023)
10-13654510-C-T		not specified	Uncertain significance (Sep 26, 2023)
10-13656641-G-A		not specified	Uncertain significance (Feb 16, 2023)
10-13656703-G-A			Likely benign (Aug 01, 2022)
10-13656707-G-A		not specified	Uncertain significance (Aug 15, 2023)
10-13656710-C-T		not specified	Uncertain significance (Aug 10, 2021)
10-13656714-A-C		not specified	Uncertain significance (Oct 04, 2022)
10-13656719-G-A		not specified	Uncertain significance (Jan 03, 2022)
10-13656727-G-T		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRPF18	protein_coding	protein_coding	ENST00000378572	10	43942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000268	0.986	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.54	87	184	0.472	0.00000980	2247
Missense in Polyphen		15	64.782	0.23155		783
Synonymous	-0.272	71	68.1	1.04	0.00000376	603
Loss of Function	2.17	9	19.3	0.467	8.12e-7	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000184
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000626	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.0000332	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in the second step of pre-mRNA splicing. {ECO:0000269|PubMed:9000057}.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.330
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.105
• hipred: Y
• hipred_score: 0.685
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.847

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prpf18
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Gene ontology

• Biological process: generation of catalytic spliceosome for second transesterification step;mRNA processing;RNA splicing;nuclear retention of unspliced pre-mRNA at the site of transcription
• Cellular component: nucleus;spliceosomal complex;U5 snRNP;nuclear speck;U4/U6 x U5 tri-snRNP complex;U2-type post-spliceosomal complex
• Molecular function: second spliceosomal transesterification activity