Is IFT172 p.Arg264= (c.792G>A) pathogenic?

IFT172 p.Arg264= (c.792G>A) is classified Likely benign in IFT172 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-16). Ultra-rare (popmax 0.0661%, mid); Associated with short-rib thoracic dysplasia 10 with or without polydactyly.

How common is IFT172 p.Arg264= (c.792G>A) in the general population?

IFT172 p.Arg264= (c.792G>A) is ultra-rare (popmax 0.0661%, mid) (gnomAD).

IFT172 p.Arg264=

Q: What condition is associated with IFT172 p.Arg264= (c.792G>A)?

IFT172 p.Arg264= (c.792G>A) is associated with short-rib thoracic dysplasia 10 with or without polydactyly, retinitis pigmentosa 71 (ClinVar).

c.792G>A · rs138730915 · VCV719814

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0661%, mid)

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.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.97	GERP -3.1, phastCons 0.002
Overall
CADD	7.122	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0661% Middle Eastern · 4/6,056 alleles

Filtering AF 0.0226% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0167%

Overall 0.00595% 96/1,613,370 alleles · ultra-rare exomes 65/1,461,130 · genomes 31/152,240 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0661%	1,514
African / African-American	0.0293%	3,408
Remaining individualsnot grpmax-eligible	0.016%	6,248
Admixed American	0.0134%	7,482
European (non-Finnish)	0.00424%	23,595
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,570
South Asian	0.0011%	91,028

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: IFT172
Protein: p.Arg264=
Coding: c.792G>A
MANE Select: NM_015662
dbSNP: rs138730915
Type: single nucleotide variant
Location: chr2:27480143 (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.Arg264Leu Uncertain significance ★★ ⚠ same residue
IFT172 p.Arg264Trp Uncertain significance ★★ ⚠ same residue
IFT172 c.1411+2T>C Likely pathogenic ★★ same condition
IFT172 c.1525-1G>A Pathogenic/Likely pathogenic ★★ same condition
IFT172 c.184-2A>C Likely pathogenic ★★ same condition
IFT172 c.2443-1G>C Likely pathogenic ★★ same condition
IFT172 c.2976-2A>T Likely pathogenic ★★ same condition
IFT172 c.3111+1G>T 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/ift172-p-arg264 (accessed [today's date]).

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