Is IFT172 p.Asp1244= (c.3732C>T) pathogenic?

IFT172 p.Asp1244= (c.3732C>T) is classified Likely benign in IFT172 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-16). Rare (popmax 0.137%, sas); Associated with short-rib thoracic dysplasia 10 with or without polydactyly.

How common is IFT172 p.Asp1244= (c.3732C>T) in the general population?

IFT172 p.Asp1244= (c.3732C>T) is rare (popmax 0.137%, sas) (gnomAD).

IFT172 p.Asp1244=

Q: What condition is associated with IFT172 p.Asp1244= (c.3732C>T)?

IFT172 p.Asp1244= (c.3732C>T) is associated with short-rib thoracic dysplasia 10 with or without polydactyly, retinitis pigmentosa 71 (ClinVar).

c.3732C>T · rs370204045 · VCV1079561

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.137%, sas)

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.
REVEL	0.454	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.7	GERP -4.8
Overall
CADD	0.481	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.137% South Asian · 125/90,952 alleles

Filtering AF 0.118% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.11%

Overall 0.00869% 140/1,611,964 alleles · rare exomes 133/1,459,810 · genomes 7/152,154 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.137%	728
Middle Eastern	0.0165%	6,072
East Asian	0.00446%	22,439
Remaining individualsnot grpmax-eligible	0.00321%	31,199
African / African-American	0.00134%	74,790
European (non-Finnish)	0.000763%	131,060

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.Asp1244=
Coding: c.3732C>T
MANE Select: NM_015662
dbSNP: rs370204045
Type: single nucleotide variant
Location: chr2:27453719 (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.Asp1244Asn 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-asp1244 (accessed [today's date]).

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