Is IFT172 p.Val1338= (c.4014A>G) pathogenic?

IFT172 p.Val1338= (c.4014A>G) is classified Benign/Likely benign in IFT172 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-03-16). Rare (popmax 0.11%, sas); Associated with Bardet-Biedl syndrome 20.

What condition is associated with IFT172 p.Val1338= (c.4014A>G)?

IFT172 p.Val1338= (c.4014A>G) is associated with Bardet-Biedl syndrome 20, short-rib thoracic dysplasia 10 with or without polydactyly, retinitis pigmentosa 71 (ClinVar).

How common is IFT172 p.Val1338= (c.4014A>G) in the general population?

IFT172 p.Val1338= (c.4014A>G) is rare (popmax 0.11%, sas) (gnomAD).

How is Bardet-Biedl syndrome inherited?

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

IFT172 p.Val1338=

c.4014A>G · rs527544045 · VCV1671940

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.11%, sas)

Conditions

Bardet-Biedl syndrome 20

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 -4.5, phastCons 0.001
Overall
CADD	1.918	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.11% South Asian · 100/91,082 alleles

Filtering AF 0.0923% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0858%

Overall 0.00644% 104/1,614,178 alleles · rare exomes 94/1,461,852 · genomes 10/152,326 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.11%	911
Remaining individualsnot grpmax-eligible	0.0048%	20,835
African / African-American	0.00133%	75,056

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.Val1338=
Coding: c.4014A>G
MANE Select: NM_015662
dbSNP: rs527544045
Type: single nucleotide variant
Location: chr2:27450034 (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

Bardet-Biedl syndrome 20 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: short-rib thoracic dysplasia 10 with or without polydactyly retinitis pigmentosa 71

For Bardet-Biedl syndrome (Orphanet):

Inheritance: Autosomal recessive, Oligogenic
Onset: Antenatal, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Specific population)

Similar variants

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
IFT172 c.786-2A>G 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-val1338 (accessed [today's date]).

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