Is IFT172 p.Thr86= (c.258T>C) pathogenic?

IFT172 p.Thr86= (c.258T>C) is classified Likely benign in IFT172 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-28). Ultra-rare (popmax 0.0882%, afr); Associated with retinitis pigmentosa 71.

What condition is associated with IFT172 p.Thr86= (c.258T>C)?

IFT172 p.Thr86= (c.258T>C) is associated with retinitis pigmentosa 71, short-rib thoracic dysplasia 10 with or without polydactyly (ClinVar).

How common is IFT172 p.Thr86= (c.258T>C) in the general population?

IFT172 p.Thr86= (c.258T>C) is ultra-rare (popmax 0.0882%, afr) (gnomAD).

How is Retinitis pigmentosa inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

IFT172 p.Thr86=

c.258T>C · rs369061009 · VCV1143230

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0882%, afr)

Conditions

retinitis pigmentosa 71

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 -0.69	GERP -4.1
Overall
CADD	7.725	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0882% African / African-American · 66/74,840 alleles

Filtering AF 0.0711% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0649%

Overall 0.00454% 73/1,606,532 alleles · ultra-rare exomes 39/1,454,360 · genomes 34/152,172 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0882%	1,134
Remaining individualsnot grpmax-eligible	0.00964%	10,370
Admixed American	0.00167%	59,994

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.Thr86=
Coding: c.258T>C
MANE Select: NM_015662
dbSNP: rs369061009
Type: single nucleotide variant
Location: chr2:27485056 (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

retinitis pigmentosa 71 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: short-rib thoracic dysplasia 10 with or without polydactyly

For Retinitis pigmentosa (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

IFT172 p.Thr86Pro 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
IFT172 c.3821+1G>A Pathogenic/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-thr86 (accessed [today's date]).

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