Menu
GeneBe

UTP14A

UTP14A small subunit processome component, the group of SSU processome

Basic information

Region (hg38): X:129906120-129929761

Previous symbols: [ "SDCCAG16" ]

Links

ENSG00000156697NCBI:10813OMIM:300508HGNC:10665Uniprot:Q9BVJ6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UTP14A gene.

  • Inborn genetic diseases (27 variants)
  • not provided (6 variants)

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
clinvar
3
missense
27
clinvar
1
clinvar
28
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 27 3 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)2524524
X-129907402-A-T not specified Uncertain significance (Jan 22, 2024)3187883
X-129907409-A-G Likely benign (Nov 01, 2023)2661405
X-129907437-G-A not specified Uncertain significance (Aug 01, 2022)2304268
X-129908063-G-T not specified Uncertain significance (Dec 02, 2022)2401978
X-129908067-A-G not specified Likely benign (Dec 20, 2023)3187876
X-129908118-A-T not specified Uncertain significance (Jun 17, 2022)2295649
X-129908679-G-C not specified Uncertain significance (Nov 13, 2023)3187879
X-129911080-A-G not specified Uncertain significance (Sep 12, 2023)2598421
X-129911796-G-A not specified Uncertain significance (Jan 09, 2024)3187882
X-129911802-G-A Benign (Feb 25, 2018)735197
X-129911826-G-A not specified Uncertain significance (Mar 20, 2023)2526799
X-129919275-G-A not specified Likely benign (Dec 22, 2023)3187884
X-129919462-G-A not specified Uncertain significance (May 27, 2022)2291980
X-129920494-G-A not specified Uncertain significance (Jul 26, 2022)2303479
X-129920506-T-A not specified Uncertain significance (Oct 26, 2022)2320854
X-129920530-C-T not specified Uncertain significance (Jul 14, 2021)2356060
X-129920561-T-C not specified Uncertain significance (Dec 05, 2022)2208374
X-129920702-A-C not specified Uncertain significance (Sep 06, 2022)2310114
X-129921206-A-G not specified Uncertain significance (Feb 03, 2022)2215248
X-129921272-G-A not specified Uncertain significance (Dec 28, 2022)2340354
X-129921284-G-T not specified Uncertain significance (Aug 08, 2023)2596794
X-129921354-C-G not specified Uncertain significance (Oct 05, 2021)2373390
X-129921425-C-A not specified Uncertain significance (Sep 01, 2021)1205987
X-129921544-G-C not specified Uncertain significance (Jan 08, 2024)3187877

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UTP14Aprotein_codingprotein_codingENST00000394422 1523641
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000168125706021257080.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.492132830.7520.00002125052
Missense in Polyphen4467.3510.65331447
Synonymous1.13911060.8600.000007751467
Loss of Function4.84129.20.03420.00000229494

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.0001340.0000993
East Asian0.000.00
Finnish0.00006250.0000462
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Utp14a
Phenotype

Gene ontology

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