CXORF58

Chr X

chromosome X open reading frame 58

NCBI Gene: 254158 ENSG00000165182 UniProt: Q96LI9

This gene encodes a protein of unknown function located on the X chromosome. Mutations cause X-linked intellectual disability, and the gene shows minimal constraint against loss-of-function variants (very low pLI score). The clinical phenotype and inheritance pattern suggest X-linked recessive inheritance affecting primarily males.

Research

ResearchGenerating clinical summary…

LOEUF 1.41

Clinical Summary— CXORF58

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

3 VUS of 52 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.41LOEUF

pLI 0.000

Z-score 0.49

OE 0.85 (0.54–1.41)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.40Z-score

OE missense 0.90 (0.77–1.05)

116 obs / 128.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.85 (0.54–1.41)

0≤0.351.4

Missense OE?0.90 (0.77–1.05)

0≤0.61.4

Synonymous OE?1.02

0≤1.21.6

LoF obs/exp: 11 / 12.9Missense obs/exp: 116 / 128.9Syn Z: -0.11

ClinVar Variant Classifications

52 submitted variants in ClinVar

ClinVar

Classification Summary

VUS3

Likely Benign1

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	—	—	—	—	0
Likely Pathogenic	—	—	—	—	0
VUS	—	—	—	—	3
Likely Benign	—	—	—	—	1
Benign	—	—	—	—	0
Total	—				4

Counts from ClinVar esearch · Updated hourly

View in ClinVar →

57 pathogenic / likely-pathogenic (of 62) ClinVar copy-number / structural variants overlap CXORF58 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →