IFT25

Chr 1

intraflagellar transport 25

Also known as: C1orf41, CFAP232, FAP232, HSPB11, HSPCO34, PP25

NCBI Gene: 51668 ENSG00000081870 UniProt: Q9Y547 OMIM: 620841

IFT25 encodes a component of intraciliary transport complex B that is required for sonic hedgehog signaling and mediates transport of signaling molecules within cilia. Mutations cause autosomal recessive ciliopathy with kidney developmental abnormalities and male infertility due to defective sperm flagella formation. The gene shows tolerance to loss-of-function variants, consistent with recessive inheritance patterns.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to enable metal ion binding activity. Predicted to be involved in kidney development; smoothened signaling pathway; and spermatogenesis. Predicted to act upstream of or within several processes, including left/right axis specification; lung development; and skeletal system development. Part of intraciliary transport particle B. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOEUF 1.35

Clinical Summary— IFT25

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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

17 VUS of 39 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?

1.35LOEUF

pLI 0.002

Z-score 0.92

OE 0.64 (0.34–1.35)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.56Z-score

OE missense 0.82 (0.66–1.01)

61 obs / 74.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.64 (0.34–1.35)

0≤0.351.4

Missense OE?0.82 (0.66–1.01)

0≤0.61.4

Synonymous OE?1.16

0≤1.21.6

LoF obs/exp: 5 / 7.8Missense obs/exp: 61 / 74.7Syn Z: -0.66

ClinVar Variant Classifications

39 submitted variants in ClinVar

ClinVar

Classification Summary

VUS17

Benign8

VUS

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	1	16	0	17
Likely Benign	0	0	0	0
Benign	0	0	8	8
Total	1	16	8	25

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

View in ClinVar →

12 pathogenic / likely-pathogenic (of 16) ClinVar copy-number / structural variants overlap IFT25 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →