Is IFT172 p.Pro438= (c.1314C>G) pathogenic?

IFT172 p.Pro438= (c.1314C>G) is classified Likely benign in IFT172 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-06-20). Very rare (popmax 0.00445%, eas); Associated with short-rib thoracic dysplasia 10 with or without polydactyly.

What condition is associated with IFT172 p.Pro438= (c.1314C>G)?

IFT172 p.Pro438= (c.1314C>G) is associated with short-rib thoracic dysplasia 10 with or without polydactyly, retinitis pigmentosa 71, Bardet-Biedl syndrome 20 (ClinVar).

How common is IFT172 p.Pro438= (c.1314C>G) in the general population?

IFT172 p.Pro438= (c.1314C>G) is very rare (popmax 0.00445%, eas) (gnomAD).

IFT172 p.Pro438=

c.1314C>G · rs1435972299 · VCV1639196

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00445%, eas)

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 1.3	GERP -4.7, phastCons 1
Overall
CADD	6.716	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00445% East Asian · 2/44,894 alleles

Filtering AF 0.000738% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000276%

Overall 0.000248% 4/1,613,274 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00445%	22,447
Admixed American	0.00167%	59,986
Remaining individualsnot grpmax-eligible	0.0016%	62,448

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.Pro438=
Coding: c.1314C>G
MANE Select: NM_015662
dbSNP: rs1435972299
Type: single nucleotide variant
Location: chr2:27477228 (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 Bardet-Biedl syndrome 20

Similar variants

IFT172 p.Pro438Leu Conflicting classifications of pathogenicity ★ 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-pro438 (accessed [today's date]).

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