PRPF39

pre-mRNA processing factor 39, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 14:45084107-45116282

Links

ENSG00000185246 ∙ NCBI:55015 ∙ OMIM:614907 ∙ HGNC:20314 ∙ Uniprot:Q86UA1 ∙ 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 PRPF39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPF39 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in PRPF39

This is a list of pathogenic ClinVar variants found in the PRPF39 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-45095337-C-T		not specified	Uncertain significance (Nov 28, 2024)
14-45095350-C-A		not specified	Uncertain significance (Sep 24, 2024)
14-45095361-T-C		not specified	Uncertain significance (Feb 28, 2024)
14-45095372-C-T		not specified	Uncertain significance (Sep 22, 2023)
14-45095494-G-C		not specified	Uncertain significance (Jul 09, 2024)
14-45096113-T-C		not specified	Uncertain significance (Jul 16, 2024)
14-45096205-G-A		not specified	Uncertain significance (May 02, 2024)
14-45102531-C-T		not specified	Uncertain significance (Oct 29, 2021)
14-45102570-G-A		not specified	Uncertain significance (Apr 06, 2022)
14-45102641-A-G		not specified	Uncertain significance (Sep 14, 2023)
14-45102660-G-A		not specified	Uncertain significance (Dec 07, 2021)
14-45107464-G-A		not specified	Uncertain significance (Oct 02, 2023)
14-45107585-C-T		not specified	Uncertain significance (Nov 14, 2024)
14-45107614-A-G		not specified	Uncertain significance (May 28, 2024)
14-45109620-A-G		not specified	Uncertain significance (Sep 20, 2023)
14-45109703-G-A		not specified	Uncertain significance (Nov 21, 2024)
14-45110103-T-C		not specified	Uncertain significance (Jan 05, 2022)
14-45110593-T-A		not specified	Uncertain significance (Apr 22, 2024)
14-45110672-A-G		not specified	Uncertain significance (Sep 16, 2021)
14-45110749-C-T		not specified	Uncertain significance (Oct 13, 2023)
14-45112364-G-T		not specified	Uncertain significance (Oct 16, 2024)
14-45112409-A-G		not specified	Uncertain significance (Mar 25, 2024)
14-45112432-A-G		not specified	Uncertain significance (Aug 14, 2024)
14-45112453-T-C		not specified	Uncertain significance (Jul 10, 2024)
14-45114909-C-A		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRPF39	protein_coding	protein_coding	ENST00000355765	13	32184

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00125	125565	0	5	125570	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.69	192	329	0.583	0.0000158	4443
Missense in Polyphen		24	66.537	0.3607		905
Synonymous	-0.109	111	110	1.01	0.00000541	1147
Loss of Function	4.81	3	32.6	0.0919	0.00000157	453

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000717	0.0000717
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.0000682	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing. {ECO:0000250}.

Recessive Scores

• pRec: 0.0861

Intolerance Scores

• loftool: 0.319
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.109
• hipred: Y
• hipred_score: 0.707
• ghis: 0.554

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.854

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prpf39

Gene ontology

• Biological process: mRNA 5'-splice site recognition
• Cellular component: commitment complex;U1 snRNP;U2-type prespliceosome
• Molecular function: pre-mRNA 5'-splice site binding