CFAP91

Chr 3AR

cilia and flagella associated protein 91

Also known as: AAT1, AAT1alpha, C3orf15, CaM-IP2, MAATS1, SPATA26, SPGF51

NCBI Gene: 89876 ENSG00000183833 UniProt: Q7Z4T9 OMIM: 609910

Involved in axonemal central apparatus assembly and spermatogenesis. Predicted to be located in motile cilium and radial spoke stalk. Implicated in spermatogenic failure 51. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

DNmechanismARLOEUF 0.891 OMIM phenotype

Clinical Summary— CFAP91

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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

4 unique Pathogenic / Likely Pathogenic· 131 VUS of 166 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?

0.89LOEUF

pLI 0.000

Z-score 2.14

OE 0.64 (0.47–0.89)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.09Z-score

OE missense 0.99 (0.91–1.07)

424 obs / 429.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.64 (0.47–0.89)

0≤0.351.4

Missense OE?0.99 (0.91–1.07)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 27 / 42.0Missense obs/exp: 424 / 429.2Syn Z: 0.29

This gene — mechanism propensity

0.7228th %ile

GOF

0.5072th %ile

LOF

0.3552th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

166 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

Likely Pathogenic3

VUS131

Likely Benign12

Benign1

Pathogenic

Likely Pathogenic

131

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	1	0	0	0	1
Likely Pathogenic	3	0	0	0	3
VUS	1	129	1	0	131
Likely Benign	0	11	0	1	12
Benign	0	1	0	0	1
Total	5	141	1	1	148

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

View in ClinVar →

14 pathogenic / likely-pathogenic (of 21) ClinVar copy-number / structural variants overlap CFAP91 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →