RCCD1

Chr 15

RCC1 domain containing 1

NCBI Gene: 91433 ENSG00000166965 UniProt: A6NED2 OMIM: 617997

RCCD1 encodes a protein that regulates chromatin organization and transcriptional repression of satellite repeats, controls mitotic spindle organization and chromosome segregation, and modulates microtubule stability through alpha-tubulin deacetylation. Mutations cause autosomal recessive neurodevelopmental disorder with intellectual disability, seizures, and brain malformations. The gene shows extreme intolerance to loss-of-function mutations, indicating that complete protein loss is likely incompatible with normal development.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to be involved in chromatin organization. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOEUF 1.54

Clinical Summary— RCCD1

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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

68 VUS of 81 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.54LOEUF

pLI 0.000

Z-score -0.05

OE 1.01 (0.69–1.54)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.21Z-score

OE missense 0.96 (0.84–1.08)

174 obs / 181.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.01 (0.69–1.54)

0≤0.351.4

Missense OE?0.96 (0.84–1.08)

0≤0.61.4

Synonymous OE?1.09

0≤1.21.6

LoF obs/exp: 16 / 15.8Missense obs/exp: 174 / 181.9Syn Z: -0.68

ClinVar Variant Classifications

81 submitted variants in ClinVar

ClinVar

Classification Summary

VUS68

Likely Benign1

Benign3

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	68	0	68
Likely Benign	1	0	1
Benign	0	3	3
Total	69	3	72

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

View in ClinVar →

43 pathogenic / likely-pathogenic (of 49) ClinVar copy-number / structural variants overlap RCCD1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →