Is IFT172 p.His439fs (c.1315dup) pathogenic?

IFT172 p.His439fs (c.1315dup) is classified Pathogenic in IFT172 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-01). No gnomAD frequency available for this variant; Associated with short-rib thoracic dysplasia 10 with or without polydactyly.

How common is IFT172 p.His439fs (c.1315dup) in the general population?

IFT172 p.His439fs (c.1315dup) is no gnomAD frequency available for this variant (gnomAD).

IFT172 p.His439fs

Q: What condition is associated with IFT172 p.His439fs (c.1315dup)?

IFT172 p.His439fs (c.1315dup) is associated with short-rib thoracic dysplasia 10 with or without polydactyly, retinitis pigmentosa 71 (ClinVar).

c.1315dup · rs2465984168 · VCV2021031

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 13 of 48
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5	GERP 0.35, 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.His439fs
Coding: c.1315dup
MANE Select: NM_015662
dbSNP: rs2465984168
Type: Duplication
Location: chr2:27477226 (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.Asp862fs Pathogenic/Likely pathogenic ★★ same condition
IFT172 p.Glu327Ter Pathogenic/Likely pathogenic ★★ same condition
IFT172 p.Ile878fs Likely pathogenic ★★ same condition
IFT172 p.Leu1597fs Pathogenic/Likely pathogenic ★★ same condition
IFT172 p.Tyr922Ter Pathogenic/Likely pathogenic ★★ same condition
IFT172 p.Val155fs Pathogenic/Likely pathogenic ★★ same condition
IFT172 p.Pro1626_Phe1627insPro Uncertain significance ★★ same condition
IFT172 c.184-23dup Benign/Likely benign ★★ 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-his439fs (accessed [today's date]).

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