UTP14C

UTP14C small subunit processome component, the group of SSU processome

Basic information

Region (hg38): 13:52024691-52033600

Previous symbols: [ "KIAA0266" ]

Links

ENSG00000253797 ∙ NCBI:9724 ∙ OMIM:608969 ∙ HGNC:20321 ∙ Uniprot:Q5TAP6 ∙ 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 UTP14C gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UTP14C 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			2	1	1	4
missense			42		3	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding	1	3	19	14	2	39
Total	1	3	63	15	6

Variants in UTP14C

This is a list of pathogenic ClinVar variants found in the UTP14C region.

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

Position	Type	Phenotype	Significance	ClinVar
13-52024711-TAAG-T		ALG11-congenital disorder of glycosylation	Conflicting classifications of pathogenicity (Aug 29, 2022)
13-52024717-G-A		ALG11-congenital disorder of glycosylation	Likely benign (May 23, 2023)
13-52024721-G-T		ALG11-congenital disorder of glycosylation	Uncertain significance (Feb 15, 2019)
13-52024738-G-A			Likely benign (Jul 23, 2018)
13-52024759-A-G		ALG11-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
13-52024762-T-G		not specified • ALG11-congenital disorder of glycosylation	Benign/Likely benign (Jan 18, 2024)
13-52024764-G-T		ALG11-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
13-52024766-C-T		ALG11-congenital disorder of glycosylation	Uncertain significance (-)
13-52024767-G-A		ALG11-congenital disorder of glycosylation	Uncertain significance (Aug 16, 2022)
13-52024804-A-G			Likely benign (Apr 23, 2018)
13-52024837-T-C		ALG11-congenital disorder of glycosylation • not specified	Benign/Likely benign (Nov 27, 2023)
13-52024851-TAAAC-T			Pathogenic (Jan 26, 2016)
13-52024872-T-C		ALG11-congenital disorder of glycosylation	Pathogenic (Mar 01, 2012)
13-52024890-A-C		ALG11-congenital disorder of glycosylation	Uncertain significance (Feb 17, 2022)
13-52024913-A-G			Uncertain significance (Feb 03, 2014)
13-52024914-T-C		ALG11-congenital disorder of glycosylation	Likely pathogenic (-)
13-52024921-C-T		ALG11-congenital disorder of glycosylation	Likely benign (Nov 30, 2020)
13-52024922-G-A		ALG11-congenital disorder of glycosylation	Pathogenic (Mar 01, 2012)
13-52024999-A-G		not specified	Benign (Jul 31, 2024)
13-52028094-T-A			Likely benign (Dec 19, 2019)
13-52028094-T-TA			Likely benign (Dec 03, 2020)
13-52028305-G-T		ALG11-congenital disorder of glycosylation	Likely benign (Dec 22, 2020)
13-52028312-T-C		ALG11-congenital disorder of glycosylation	Likely benign (Dec 22, 2020)
13-52028313-T-C		ALG11-congenital disorder of glycosylation	Conflicting classifications of pathogenicity (Aug 17, 2023)
13-52028325-T-C		ALG11-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UTP14C	protein_coding	protein_coding	ENST00000521776	1	8910

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00535	0.994	125547	1	200	125748	0.000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.472	398	372	1.07	0.0000197	5049
Missense in Polyphen		104	99.541	1.0448		1532
Synonymous	0.601	136	145	0.937	0.00000782	1476
Loss of Function	2.88	8	22.9	0.350	0.00000118	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000514	0.000514
Ashkenazi Jewish	0.00576	0.00567
East Asian	0.000762	0.000761
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000422	0.000422
Middle Eastern	0.000762	0.000761
South Asian	0.00353	0.00213
Other	0.000816	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for spermatogenesis. May be required specifically for ribosome biogenesis and hence protein synthesis during male meiosis (By similarity). {ECO:0000250, ECO:0000269|PubMed:15289605}.
• 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)

Intolerance Scores

• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.1

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.158
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.247

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Utp14b
• Phenotype: reproductive system 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); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: rRNA processing;multicellular organism development;spermatogenesis;cell differentiation;meiotic cell cycle
• Cellular component: nucleolus;cytosol;small-subunit processome
• Molecular function: protein binding