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NEPRO

Chr 3AR

ribonuclease MRP subunit p64

Also known as: ANXD3, C3orf17, NEPRO, NET17

NCBI Gene: 25871 UniProt: Q6NW34 OMIM: 617089

NEPRO encodes a component of the MRP ribonucleoprotein complex involved in pre-rRNA processing and may regulate cortex development through the Notch signaling pathway by inhibiting neuronal differentiation. Biallelic mutations cause anauxetic dysplasia 3, an autosomal recessive skeletal dysplasia syndrome. The gene shows low constraint against loss-of-function variants, consistent with recessive inheritance.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

Predicted to enable RNA binding activity. Involved in RNA processing. Located in nucleolus and nucleoplasm. Part of ribonuclease MRP complex. Implicated in anauxetic dysplasia 3. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Anauxetic dysplasia 3MIM #618853

Clinical highlights

Gene–disease validity

Not independently assessedOMIM lists Anauxetic dysplasia 3; no ClinGen or GenCC tier

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.97

LOEUF

—

Mechanism

Some data sources returned errors (1)

ensembl: Error: Ensembl fetch failed: 400 for /lookup/symbol/homo_sapiens/NEPRO?content-type=application/json

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.97LOEUF

pLI 0.000

Z-score 1.68

OE 0.64 (0.43–0.97)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-0.09Z-score

OE missense 1.01 (0.92–1.12)

299 obs / 294.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.64 (0.43–0.97)

0≤0.351.4

Missense OE?1.01 (0.92–1.12)

0≤0.61.4

Synonymous OE?0.86

0≤1.21.6

LoF obs/exp: 16 / 25.1Missense obs/exp: 299 / 294.7Syn Z: 1.17

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

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 95

690 rare PASS variants

Rare truncating (LoF)

1 in 540

153 rare PASS variants

Rare synonymous (reference)

1 in 190

230 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for NEPRO. 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 120	1 in 600
South Asian	~43k	1 in 78	1 in 500
Remaining (unassigned)	~30k	1 in 90	1 in 330
European (Finnish)	~27k	1 in 310	1 in 3,300
Admixed American	~22k	1 in 64	1 in 800
African / African American	~21k	1 in 73	1 in 990
East Asian	~20k	1 in 90	1 in 280
Ashkenazi Jewish	~13k	1 in 270	≈ 1 in 6,400
Middle Eastern	~2,884	1 in 83	≈ 1 in 720

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.