Is IFT52 p.Ile307= (c.921C>T) pathogenic?

IFT52 p.Ile307= (c.921C>T) is classified Likely benign in IFT52 (ClinVar, No assertion criteria, 2 submitters; last evaluated 2019-09-17). Ultra-rare (popmax 0.0165%, mid); Associated with IFT52-related disorder.

What condition is associated with IFT52 p.Ile307= (c.921C>T)?

IFT52 p.Ile307= (c.921C>T) is associated with IFT52-related disorder (ClinVar).

How common is IFT52 p.Ile307= (c.921C>T) in the general population?

IFT52 p.Ile307= (c.921C>T) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

IFT52 p.Ile307=

c.921C>T · rs1199174261 · VCV3040968

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Conditions

IFT52-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.5	GERP 1.5, phastCons 1
Overall
CADD	17.45	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,056 alleles

Overall 6.2e-05% 1/1,613,938 alleles · ultra-rare exomes 1/1,461,692 · genomes 0/152,246 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: IFT52
Protein: p.Ile307=
Coding: c.921C>T
MANE Select: NM_016004
dbSNP: rs1199174261
Type: single nucleotide variant
Location: chr20:43624043 (GRCh38)
Gene constraint: LOEUF 1.116 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.21

Full IFT52 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

IFT52-related disorder

Similar variants

IFT52 p.Asn35Ser Uncertain significance ★★ ⚠ same type
IFT52 p.Glu4Asp Uncertain significance ★★ ⚠ same type
IFT52 p.Gly134Glu Uncertain significance ★★ ⚠ same type
IFT52 p.Leu164Phe Uncertain significance ★★ ⚠ same type
IFT52 p.Leu334Arg Uncertain significance ★★ same type
IFT52 p.Phe95Ser Uncertain significance ★★ ⚠ same type
IFT52 p.Pro397Ser Uncertain significance ★★ ⚠ same type
IFT52 p.Val53Met Uncertain significance ★★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ift52-p-ile307 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown