UTP14A

UTP14A small subunit processome component, the group of SSU processome

Basic information

Region (hg38): X:129906120-129929761

Previous symbols: [ "SDCCAG16" ]

Links

ENSG00000156697 ∙ NCBI:10813 ∙ OMIM:300508 ∙ HGNC:10665 ∙ Uniprot:Q9BVJ6 ∙ 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 UTP14A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UTP14A 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				3		3
missense			34	2	1	37
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	34	5	1

Variants in UTP14A

This is a list of pathogenic ClinVar variants found in the UTP14A region.

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

Position	Type	Phenotype	Significance	ClinVar
X-129907374-G-A		not specified	Uncertain significance (Jun 02, 2023)
X-129907402-A-T		not specified	Uncertain significance (Jan 22, 2024)
X-129907409-A-G			Likely benign (Nov 01, 2023)
X-129907437-G-A		not specified	Uncertain significance (Aug 01, 2022)
X-129908063-G-T		not specified	Uncertain significance (Dec 02, 2022)
X-129908067-A-G		not specified	Likely benign (Dec 20, 2023)
X-129908118-A-T		not specified	Uncertain significance (Jun 17, 2022)
X-129908679-G-C		not specified	Uncertain significance (Nov 13, 2023)
X-129911080-A-G		not specified	Uncertain significance (Sep 12, 2023)
X-129911796-G-A		not specified	Uncertain significance (Jan 09, 2024)
X-129911802-G-A			Benign (Feb 25, 2018)
X-129911826-G-A		not specified	Uncertain significance (Mar 20, 2023)
X-129919275-G-A		not specified	Likely benign (Dec 22, 2023)
X-129919462-G-A		not specified	Uncertain significance (May 27, 2022)
X-129920494-G-A		not specified	Uncertain significance (Jul 26, 2022)
X-129920506-T-A		not specified	Uncertain significance (Oct 26, 2022)
X-129920530-C-T		not specified	Uncertain significance (Jul 14, 2021)
X-129920561-T-C		not specified	Uncertain significance (Dec 05, 2022)
X-129920702-A-C		not specified	Uncertain significance (Sep 06, 2022)
X-129921206-A-G		not specified	Uncertain significance (Feb 03, 2022)
X-129921272-G-A		not specified	Uncertain significance (Dec 28, 2022)
X-129921284-G-T		not specified	Uncertain significance (Aug 08, 2023)
X-129921354-C-G		not specified	Uncertain significance (Oct 05, 2021)
X-129921425-C-A		not specified	Uncertain significance (Sep 01, 2021)
X-129921544-G-C		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UTP14A	protein_coding	protein_coding	ENST00000394422	15	23641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000168	125706	0	2	125708	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	213	283	0.752	0.0000212	5052
Missense in Polyphen		44	67.351	0.6533		1447
Synonymous	1.13	91	106	0.860	0.00000775	1467
Loss of Function	4.84	1	29.2	0.0342	0.00000229	494

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000134	0.0000993
East Asian	0.00	0.00
Finnish	0.0000625	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be required for ribosome biogenesis. {ECO:0000250}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.0965

Intolerance Scores

• loftool: 0.141
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.31

Haploinsufficiency Scores

• pHI: 0.429
• hipred: N
• hipred_score: 0.423
• ghis: 0.566

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.602

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Utp14a

Gene ontology

• Biological process: rRNA processing
• Cellular component: nucleoplasm;nucleolus;cytosol;small-subunit processome
• Molecular function: RNA binding;protein binding