UTP14A

protein-coding

UTP14A small subunit processome component, the group of SSU processome

Gene summary

This gene encodes a member of the uridine triphosphate 14 family. As an essential component of a large ribonucleoprotein complex bound to the U3 small nucleolar RNA, the encoded protein is involved in ribosome biogenesis and 18S rRNA synthesis. An autosomal retrotransposed copy of this X-linked gene exists on chromosome 13. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]

Previous symbols:

SDCCAG16

MANE transcript

NM_006649.4

Inheritance

—

ClinVar variants

U:179B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chrX:129,906,121-129,929,761

External References & Databases

Ensembl (ENSG00000156697)

Transcript & Mutation Effects

hg38 • Region Span ~23.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UTP14A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 73

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006649.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			17 clinvar	4 clinvar		21
missense			125 clinvar	5 clinvar	1 clinvar	131
nonsense			12 clinvar			12
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			25 clinvar			25
Total	0	0	179	9	1	189

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006649.4	RefSeq	NP_006640.2	15	MANE Select
ENST00000394422.8	Ensembl	ENSP00000377944.3	15	MANE Select
NM_001166221.2	RefSeq	NP_001159693.1	14	Standard
ENST00000425117.6	Ensembl	ENSP00000388669.2	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

rRNA processing

Molecular Function

RNA binding
protein binding

Cellular Component

nucleoplasm
nucleolus
cytosol
small-subunit processome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394422
Coding exons: 15
Length: 23641
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125708
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.49	213	283	0.752	0.0000212	5052
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00013	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000062	0.000046	rare
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be required for ribosome biogenesis. {ECO:0000250}.;

Recessive Scores

pRec: 0.0965

Intolerance Scores

LoFtool: 0.141
RVIS EVS: 0.4
RVIS percentile EVS: 76.31

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.602

Gene Damage Prediction

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