CIMIP2A

Chr 9

ciliary microtubule inner protein 2A

Also known as: FAM166A, HSD46

The protein is a microtubule inner protein that binds to intra-tubulin interfaces within dynein-decorated doublet microtubules in flagellar axonemes and is involved in flagellated sperm motility. Mutations cause primary ciliary dyskinesia with an autosomal recessive inheritance pattern. The gene shows minimal constraint against loss-of-function variants based on population genetics data.

ResearchSummary from RefSeq, UniProt

Predicted to be involved in flagellated sperm motility. Located in ciliary basal body. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

LOEUF 1.66

Clinical Summary— CIMIP2A

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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

98 VUS of 119 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?

1.66LOEUF

pLI 0.000

Z-score -0.42

OE 1.12 (0.76–1.66)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-2.21Z-score

OE missense 1.44 (1.31–1.59)

287 obs / 199.3 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.12 (0.76–1.66)

0≤0.351.4

Missense OE?1.44 (1.31–1.59)

0≤0.61.4

Synonymous OE?1.33

0≤1.21.6

LoF obs/exp: 17 / 15.2Missense obs/exp: 287 / 199.3Syn Z: -2.36

ClinVar Variant Classifications

119 submitted variants in ClinVar

ClinVar

Classification Summary

VUS98

Likely Benign10

Benign3

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	0	98	0	98
Likely Benign	0	8	2	10
Benign	1	2	0	3
Total	1	108	2	111

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

View in ClinVar →

98 pathogenic / likely-pathogenic (of 110) ClinVar copy-number / structural variants overlap CIMIP2A — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →