UTP25

UTP25 small subunit processome component, the group of SSU processome

Basic information

Region (hg38): 1:209827972-209857565

Previous symbols: [ "C1orf107", "DIEXF" ]

Links

ENSG00000117597 ∙ NCBI:27042 ∙ OMIM:619663 ∙ HGNC:28440 ∙ Uniprot:Q68CQ4 ∙ 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 UTP25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UTP25 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			46			46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	0	0

Variants in UTP25

This is a list of pathogenic ClinVar variants found in the UTP25 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-209828086-G-A		not specified	Uncertain significance (Aug 13, 2021)
1-209828107-C-T		not specified	Uncertain significance (Dec 04, 2024)
1-209828133-C-T		not specified	Uncertain significance (Jul 20, 2022)
1-209830110-T-C		not specified	Uncertain significance (Oct 16, 2024)
1-209830140-G-C		not specified	Uncertain significance (Mar 28, 2024)
1-209830876-G-C		not specified	Uncertain significance (May 01, 2024)
1-209830888-C-A		not specified	Uncertain significance (Oct 06, 2021)
1-209830892-A-C		not specified	Uncertain significance (Sep 30, 2024)
1-209830933-A-G		not specified	Uncertain significance (Jul 25, 2024)
1-209830958-T-G		not specified	Uncertain significance (Apr 18, 2024)
1-209830967-A-T		not specified	Uncertain significance (Aug 28, 2024)
1-209830974-G-A		not specified	Uncertain significance (Oct 13, 2023)
1-209830999-G-A		not specified	Uncertain significance (Feb 07, 2023)
1-209831016-G-A		not specified	Uncertain significance (Jul 10, 2024)
1-209833218-A-G		not specified	Uncertain significance (Sep 29, 2022)
1-209833259-G-A		not specified	Uncertain significance (Dec 22, 2023)
1-209833289-C-G		not specified	Uncertain significance (Oct 12, 2021)
1-209833326-G-A		not specified	Uncertain significance (Jul 12, 2023)
1-209833355-C-G		not specified	Uncertain significance (Feb 17, 2023)
1-209836832-C-G		not specified	Uncertain significance (Oct 10, 2023)
1-209836859-A-G		not specified	Uncertain significance (Feb 11, 2022)
1-209836864-C-T		not specified	Uncertain significance (Mar 28, 2024)
1-209836951-C-T		not specified	Uncertain significance (Oct 20, 2021)
1-209836981-C-G		not specified	Uncertain significance (Nov 21, 2023)
1-209837003-T-A		not specified	Uncertain significance (May 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UTP25	protein_coding	protein_coding	ENST00000491415	12	29559

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000124	1.00	125679	0	69	125748	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.575	376	409	0.920	0.0000216	5022
Missense in Polyphen		90	118.43	0.75997		1374
Synonymous	0.247	156	160	0.975	0.00000884	1406
Loss of Function	3.06	16	35.7	0.448	0.00000183	423

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000954	0.000952
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000310	0.000308
Middle Eastern	0.000326	0.000326
South Asian	0.0000653	0.0000653
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates the p53 pathway to control the expansion growth of digestive organs. {ECO:0000250}.

Recessive Scores

• pRec: 0.231

Intolerance Scores

• rvis_EVS: 1.03
• rvis_percentile_EVS: 91.07

Haploinsufficiency Scores

• pHI: 0.391
• hipred: N
• hipred_score: 0.492
• ghis: 0.491

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Diexf

Zebrafish Information Network

• Gene name: utp25
• Affected structure: gut epithelium
• Phenotype tag: abnormal
• Phenotype quality: morphology