Is IFT74 p.Ala584= (c.1752A>C) pathogenic?

IFT74 p.Ala584= (c.1752A>C) is classified Likely benign in IFT74 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-06-15). Absent from gnomAD v4.1; Associated with IFT74-related disorder.

What condition is associated with IFT74 p.Ala584= (c.1752A>C)?

IFT74 p.Ala584= (c.1752A>C) is associated with IFT74-related disorder (ClinVar).

How common is IFT74 p.Ala584= (c.1752A>C) in the general population?

IFT74 p.Ala584= (c.1752A>C) is absent from gnomAD v4.1 (gnomAD).

IFT74 p.Ala584=

c.1752A>C · VCV3353415

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

IFT74-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.3	GERP -0.65, phastCons 1
Overall
CADD	8.485	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: IFT74
Protein: p.Ala584=
Coding: c.1752A>C
MANE Select: NM_025103
Type: single nucleotide variant
Location: chr9:27062685 (GRCh38)
Gene constraint: LOEUF 1.508 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.21
Residue 584: a UniProt-annotated variant site (in jbts40); the 'important for interaction with ift27' region

Full IFT74 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

IFT74-related disorder

Similar variants

IFT74 p.Ala584Ser Uncertain significance ★ ⚠ same residue
IFT74 c.1685-1G>T Pathogenic/Likely pathogenic ★★ same condition
IFT74 p.Thr327Lys Uncertain significance ★★ ⚠ same condition
IFT74 p.Gln342Ter Conflicting classifications of pathogenicity ★ same condition
IFT74 p.Arg288Ter Likely pathogenic same condition
IFT74 c.1054+7363T>C Uncertain significance same condition
IFT74 c.1054+7400A>C Uncertain significance same condition
IFT74 c.1054+7405G>A Uncertain significance same condition

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/ift74-p-ala584 (accessed [today's date]).

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