CFAP97

Chr 4

cilia and flagella associated protein 97

Also known as: KIAA1430, hmw

NCBI Gene: 57587 ENSG00000164323 UniProt: Q9P2B7 OMIM: 616047

CFAP97 encodes a cilia and flagella associated protein that is essential for proper ciliary structure and function. Mutations cause primary ciliary dyskinesia, an autosomal recessive disorder characterized by chronic respiratory infections, bronchiectasis, and situs inversus due to defective ciliary motility. The gene shows minimal constraint against loss-of-function variants, consistent with the recessive inheritance pattern where heterozygous carriers are typically unaffected.

OMIM Research

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 0.93

Clinical Summary— CFAP97

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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

94 VUS of 119 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.93LOEUF

pLI 0.000

Z-score 1.78

OE 0.53 (0.32–0.93)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-0.23Z-score

OE missense 1.04 (0.94–1.15)

284 obs / 273.4 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.53 (0.32–0.93)

0≤0.351.4

Missense OE?1.04 (0.94–1.15)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 9 / 16.9Missense obs/exp: 284 / 273.4Syn Z: -0.04

This gene — mechanism propensity

0.6550th %ile

GOF

0.4579th %ile

LOF

0.4037th %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

119 submitted variants in ClinVar

ClinVar

Classification Summary

VUS94

Likely Benign9

Benign4

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	94	0	94
Likely Benign	7	2	9
Benign	1	3	4
Total	102	5	107

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

View in ClinVar →

113 pathogenic / likely-pathogenic (of 142) ClinVar copy-number / structural variants overlap CFAP97 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →