CFAP45

Chr 1AR

cilia and flagella associated protein 45

Also known as: CCDC19, HTX11, NESG1

NCBI Gene: 25790 ENSG00000213085 UniProt: Q9UL16 OMIM: 605152

Enables AMP binding activity. Involved in establishment of left/right asymmetry and flagellated sperm motility. Located in axonemal microtubule and sperm flagellum. Implicated in visceral heterotaxy 11. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

DNmechanismARLOEUF 1.001 OMIM phenotype

Clinical Summary— CFAP45

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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

5 unique Pathogenic / Likely Pathogenic· 107 VUS of 131 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?

1.00LOEUF

pLI 0.000

Z-score 1.57

OE 0.72 (0.53–1.00)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-0.55Z-score

OE missense 1.08 (0.99–1.18)

356 obs / 328.1 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.72 (0.53–1.00)

0≤0.351.4

Missense OE?1.08 (0.99–1.18)

0≤0.61.4

Synonymous OE?0.86

0≤1.21.6

LoF obs/exp: 26 / 36.2Missense obs/exp: 356 / 328.1Syn Z: 1.18

This gene — mechanism propensity

0.83top 10%

GOF

0.6052th %ile

LOF

0.2678th %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

131 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4

Likely Pathogenic1

VUS107

Likely Benign9

Benign1

Pathogenic

Likely Pathogenic

107

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Synonymous	Total
Pathogenic	4	0	0	4
Likely Pathogenic	1	0	0	1
VUS	0	107	0	107
Likely Benign	0	5	4	9
Benign	0	1	0	1
Total	5	113	4	122

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

View in ClinVar →

9 pathogenic / likely-pathogenic (of 14) ClinVar copy-number / structural variants overlap CFAP45 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →