INO80D

Chr 2

INO80 complex subunit D

NCBI Gene: 54891 ENSG00000114933 UniProt: Q53TQ3 OMIM: 619207

The protein is a regulatory component of the INO80 chromatin remodeling complex, which controls gene transcription, DNA replication, and DNA repair. This gene is highly constrained against loss-of-function mutations (pLI 1.0, LOEUF 0.23), suggesting mutations would likely cause severe developmental disorders, though specific associated diseases have not yet been clearly established in the literature. The inheritance pattern for potential INO80D-related conditions remains to be determined.

OMIM ResearchSummary from RefSeq, UniProt

Involved in several processes, including chromatin remodeling; regulation of chromosome organization; and regulation of nucleobase-containing compound metabolic process. Part of Ino80 complex. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.23

Clinical Summary— INO80D

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

117 VUS of 134 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.23LOEUF

pLI 1.000

Z-score 5.29

OE 0.10 (0.05–0.23)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

2.74Z-score

OE missense 0.68 (0.62–0.74)

390 obs / 575.1 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.10 (0.05–0.23)

0≤0.351.4

Missense OE?0.68 (0.62–0.74)

0≤0.61.4

Synonymous OE?0.99

0≤1.21.6

LoF obs/exp: 4 / 40.2Missense obs/exp: 390 / 575.1Syn Z: 0.12

This gene — mechanism propensity

0.2499th %ile

GOF

0.2298th %ile

LOF

0.84top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.23

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

134 submitted variants in ClinVar

ClinVar

Classification Summary

VUS117

Likely Benign2

Benign2

117

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	116	1	117
Likely Benign	2	0	2
Benign	2	0	2
Total	120	1	121

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

25 pathogenic / likely-pathogenic (of 31) ClinVar copy-number / structural variants overlap INO80D — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →