CFAP44

Chr 3AR

cilia and flagella associated protein 44

Also known as: SPGF20, WDR52

NCBI Gene: 55779 ENSG00000206530 UniProt: Q96MT7 OMIM: 617559

This protein is involved in sperm flagellum axoneme organization and function, enabling peptidase activity required for proper sperm motility. Mutations cause spermatogenic failure 20, inherited in an autosomal recessive pattern. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.561), and while primarily associated with male fertility issues, variants may be identified in pediatric patients during genetic evaluations.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

Enables peptidase activity. Involved in sperm axoneme assembly. Acts upstream of or within microtubule cytoskeleton organization. Predicted to be located in cytoplasm; cytoskeleton; and motile cilium. Implicated in spermatogenic failure 20. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

ARLOEUF 0.561 OMIM phenotype

Clinical Summary— CFAP44

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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

16 unique Pathogenic / Likely Pathogenic· 115 VUS of 243 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.56LOEUF

pLI 0.000

Z-score 5.12

OE 0.43 (0.34–0.56)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.37Z-score

OE missense 0.87 (0.82–0.93)

801 obs / 917.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.43 (0.34–0.56)

0≤0.351.4

Missense OE?0.87 (0.82–0.93)

0≤0.61.4

Synonymous OE?0.90

0≤1.21.6

LoF obs/exp: 41 / 94.8Missense obs/exp: 801 / 917.6Syn Z: 1.41

ClinVar Variant Classifications

243 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic9

Likely Pathogenic7

VUS115

Likely Benign49

Benign19

Conflicting7

Pathogenic

Likely Pathogenic

115

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	7	1	1	0	9
Likely Pathogenic	7	0	0	0	7
VUS	0	115	0	0	115
Likely Benign	1	15	6	27	49
Benign	0	9	2	8	19
Conflicting	—				7
Total	15	140	9	35	206

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

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29 pathogenic / likely-pathogenic (of 32) ClinVar copy-number / structural variants overlap CFAP44 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →