CCDC90B

Chr 11

coiled-coil domain containing 90B

Also known as: MDS011, MDS025

NCBI Gene: 60492 ENSG00000137500 UniProt: Q9GZT6

CCDC90B encodes a mitochondrial protein of unknown specific function. Mutations cause autosomal recessive spastic paraplegia with intellectual disability and seizures, typically presenting in early childhood. The gene shows minimal constraint against loss-of-function variants, consistent with recessive inheritance where heterozygous carriers are unaffected.

ResearchSummary from RefSeq

Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.10

LOEUF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.10LOEUF

pLI 0.000

Z-score 1.28

OE 0.65 (0.40–1.10)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.00Z-score

OE missense 1.00 (0.87–1.16)

128 obs / 127.9 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.65 (0.40–1.10)

0≤0.351.4

Missense OE?1.00 (0.87–1.16)

0≤0.61.4

Synonymous OE?1.21

0≤1.21.6

LoF obs/exp: 10 / 15.4Missense obs/exp: 128 / 127.9Syn Z: -1.12

Background carrier burden — how many people carry a rare variant somewhere in CCDC90B?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

409 rare PASS variants

Rare truncating (LoF)

1 in 400

106 rare PASS variants

Rare synonymous (reference)

1 in 600

123 rare PASS variants

Rare missense and truncating variants are carried at similar rates in CCDC90B; 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 120	1 in 510
South Asian	~43k	1 in 170	1 in 370
Remaining (unassigned)	~30k	1 in 91	1 in 550
European (Finnish)	~27k	1 in 500	1 in 740
Admixed American	~22k	1 in 89	1 in 1,200
African / African American	~21k	1 in 86	1 in 290
East Asian	~20k	1 in 150	1 in 430
Ashkenazi Jewish	~13k	1 in 410	1 in 320
Middle Eastern	~2,883	1 in 140	1 in 550

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 5 of 9 coding exons well covered in gnomAD exomes; exons 4, 5, 8, 9 marginal. Genomes: all 9.? see exons ↓