NOP10

Chr 15

NOP10 ribonucleoprotein

Also known as: CHINE2, DKCB1, NOLA3, NOP10P, PFBMFT9

NCBI Gene: 55505 ENSG00000182117 UniProt: Q9NPE3

This gene is a member of the H/ACA snoRNPs (small nucleolar ribonucleoproteins) gene family. snoRNPs are involved in various aspects of rRNA processing and modification and have been classified into two families: C/D and H/ACA. The H/ACA snoRNPs also include the DKC1, NOLA1 and NOLA2 proteins. These four H/ACA snoRNP proteins localize to the dense fibrillar components of nucleoli and to coiled (Cajal) bodies in the nucleus. Both 18S rRNA production and rRNA pseudouridylation are impaired if any one of the four proteins is depleted. The four H/ACA snoRNP proteins are also components of the telomerase complex. This gene encodes a protein related to Saccharomyces cerevisiae Nop10p. [provided by RefSeq, Jul 2008]

GeneReviews Research

GeneReviews ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtDyskeratosis congenita, autosomal recessive, 1

UniProtCataracts, hearing impairment, nephrotic syndrome, and enterocolitis 2

UniProtPulmonary fibrosis, and/or bone marrow failure syndrome, telomere-related, 9

Clinical highlights

Gene–disease validity (ClinGen)

Limited · pulmonary fibrosis and/or bone marrow failure syndrome, telomere-related, 9 · AD · ClinGen 2025

not for standalone diagnostic reporting

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.62

LOEUF

LOF

Mechanism· G2P

📖

GeneReview available — NOP10

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.62LOEUF

pLI 0.769

Z-score 2.04

OE 0.00 (0.00–0.62)

Moderately constrained

Typical tolerance to LoF variation

Missense Constraint?

0.32Z-score

OE missense 0.86 (0.65–1.15)

33 obs / 38.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.62)

0≤0.351.4

Missense OE?0.86 (0.65–1.15)

0≤0.61.4

Synonymous OE?0.68

0≤1.21.6

LoF obs/exp: 0 / 4.9Missense obs/exp: 33 / 38.5Syn Z: 0.97

Background carrier burden — how many people carry a rare variant somewhere in NOP10?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 2,300

84 rare PASS variants

Rare truncating (LoF)

1 in 3,600

19 rare PASS variants

Rare synonymous (reference)

1 in 3,600

24 rare PASS variants

Rare missense and truncating variants are carried at similar rates in NOP10; this gene does not show strong loss-of-function constraint by this measure. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 2,300	1 in 3,100
South Asian	~43k	1 in 2,100	1 in 2,000
Remaining (unassigned)	~30k	1 in 2,500	≈ 1 in 15,000
European (Finnish)	~27k	1 in 3,800	none seen
Admixed American	~22k	1 in 2,800	none seen
African / African American	~21k	1 in 2,200	≈ 1 in 6,000
East Asian	~20k	1 in 1,300	1 in 2,100
Ashkenazi Jewish	~13k	≈ 1 in 13,000	none seen
Middle Eastern	~2,884	≈ 1 in 1,400	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.