UTP14A
Basic information
Region (hg38): X:129906120-129929761
Previous symbols: [ "SDCCAG16" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 34 | 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:
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:
- 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
- Phenotype
Gene ontology
- Biological process
- rRNA processing
- Cellular component
- nucleoplasm;nucleolus;cytosol;small-subunit processome
- Molecular function
- RNA binding;protein binding