Is IFT172 p.Phe403fs (c.1209del) pathogenic?

IFT172 p.Phe403fs (c.1209del) is classified Pathogenic in IFT172 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-23). No gnomAD frequency available for this variant; Associated with short-rib thoracic dysplasia 10 with or without polydactyly.

How common is IFT172 p.Phe403fs (c.1209del) in the general population?

IFT172 p.Phe403fs (c.1209del) is no gnomAD frequency available for this variant (gnomAD).

IFT172 p.Phe403fs

Q: What condition is associated with IFT172 p.Phe403fs (c.1209del)?

IFT172 p.Phe403fs (c.1209del) is associated with short-rib thoracic dysplasia 10 with or without polydactyly, retinitis pigmentosa 71 (ClinVar).

c.1209del · rs2148542989 · VCV1390470

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

short-rib thoracic dysplasia 10 with or without polydactyly

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 12 of 48
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 2.3, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: IFT172
Protein: p.Phe403fs
Coding: c.1209del
MANE Select: NM_015662
dbSNP: rs2148542989
Type: Deletion
Location: chr2:27477571 (GRCh38)
Gene constraint: LOEUF 0.745 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.98 · 1 PDB

Full IFT172 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

short-rib thoracic dysplasia 10 with or without polydactyly — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: retinitis pigmentosa 71

Similar variants

IFT172 p.Arg720fs Pathogenic/Likely pathogenic ★★ same condition
IFT172 p.Glu359_Val360insTer Pathogenic/Likely pathogenic ★★ same condition
IFT172 p.Leu818_Phe819insTer Pathogenic/Likely pathogenic ★★ same condition
IFT172 p.Leu856fs Pathogenic/Likely pathogenic ★★ same condition
IFT172 p.Thr624fs Pathogenic/Likely pathogenic ★★ same condition
IFT172 p.Asn446del Uncertain significance ★★ same condition
IFT172 p.Leu891_Ala893del Uncertain significance ★★ same condition
IFT172 p.Pro1254_Ser1255del 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/ift172-p-phe403fs (accessed [today's date]).

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