Is IFT80 p.Val71= (c.213A>C) pathogenic?

IFT80 p.Val71= (c.213A>C) is classified Likely benign in IFT80 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-22). Ultra-rare (popmax 0.048%, afr); Associated with Jeune syndrome.

What condition is associated with IFT80 p.Val71= (c.213A>C)?

IFT80 p.Val71= (c.213A>C) is associated with Jeune syndrome (ClinVar).

How common is IFT80 p.Val71= (c.213A>C) in the general population?

IFT80 p.Val71= (c.213A>C) is ultra-rare (popmax 0.048%, afr) (gnomAD).

IFT80 p.Val71=

c.213A>C · rs560970159 · VCV700782

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.048%, afr)

Conditions

Jeune syndrome

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 0.28	GERP -2.8, phastCons 0.079
Overall
CADD	2.399	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.048% African / African-American · 36/75,020 alleles

Filtering AF 0.0356% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0313%

Overall 0.0102% 165/1,613,930 alleles · ultra-rare exomes 140/1,461,680 · genomes 25/152,250 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.048%	2,084
Admixed American	0.0416%	2,401
Remaining individualsnot grpmax-eligible	0.0336%	2,976
Middle Eastern	0.0166%	6,026
European (non-Finnish)	0.00695%	14,389

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: IFT80
Protein: p.Val71=
Coding: c.213A>C
MANE Select: NM_020800
dbSNP: rs560970159
Type: single nucleotide variant
Location: chr3:160381549 (GRCh38)
Gene constraint: LOEUF 0.739 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.50

Full IFT80 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Jeune syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

IFT80 p.Arg495Ter Pathogenic/Likely pathogenic ★★ same condition
IFT80 p.Trp155Ter Pathogenic/Likely pathogenic ★★ same condition
IFT80 c.1076+6C>A Uncertain significance ★★ same condition
IFT80 c.1836+5T>C Uncertain significance ★★ same condition
IFT80 c.370+6T>C Uncertain significance ★★ same condition
IFT80 p.Ala154Val Uncertain significance ★★ ⚠ same condition
IFT80 p.Ala236Val Uncertain significance ★★ ⚠ same condition
IFT80 p.Arg220Cys Uncertain significance ★★ ⚠ 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/ift80-p-val71 (accessed [today's date]).

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