Is IFT54 p.Arg211fs (c.632_633del) pathogenic?

IFT54 p.Arg211fs (c.632633del) is classified Likely pathogenic in IFT54 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-27). Associated with TRAF3IP1-related disorder.

What condition is associated with IFT54 p.Arg211fs (c.632_633del)?

IFT54 p.Arg211fs (c.632_633del) is associated with TRAF3IP1-related disorder (ClinVar).

IFT54 p.Arg211fs

c.632_633del · VCV4960779

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

TRAF3IP1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 5 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.15	GERP -2.4, phastCons 0.56

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: IFT54
Protein: p.Arg211fs
Coding: c.632_633del
MANE Select: NM_015650
Type: Deletion
Location: chr2:238329058 (GRCh38)
Structure: AlphaFold pLDDT 61.95 · 2 PDB
Residue 211: the 'abolishes microtubules-binding when missing' region; the 'disordered' region

Full IFT54 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

TRAF3IP1-related disorder

Similar variants

IFT54 p.Glu497fs Pathogenic/Likely pathogenic ★★ same condition
IFT54 p.Ala391fs Likely pathogenic ★ same condition
IFT54 c.1159+1G>C Likely pathogenic ★★ same condition
IFT54 c.988-1G>A Likely pathogenic ★★ same condition
IFT54 c.988-1G>C Likely pathogenic ★★ same condition
IFT54 p.Trp572Ter Pathogenic/Likely pathogenic ★★ same condition
IFT54 p.Arg182Ter Likely pathogenic ★ same condition
IFT54 p.Arg348Ter Likely pathogenic ★ 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/ift54-p-arg211fs (accessed [today's date]).

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