IFT80 p.Ser248=
c.744G>A · rs779731718 · VCV1664186
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00833%, amr)
Conditions
1
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 -8.6 | GERP -3.2 |
| Overall | ||
| CADD | 5.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00833%
Admixed American · 5/59,998 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00143%
23/1,613,936 alleles · very rare
exomes 20/1,461,776 · genomes 3/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00833% | 12,000 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,620 |
| South Asian | 0.00439% | 22,770 |
| East Asian | 0.00223% | 44,884 |
| African / African-American | 0.00133% | 74,918 |
| European (non-Finnish) | 0.000678% | 147,498 |
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.Ser248=
- Coding
- c.744G>A
- MANE Select
- NM_020800
- dbSNP
- rs779731718
- Type
- single nucleotide variant
- Location
- chr3:160356046 (GRCh38)
- Gene constraint
- LOEUF 0.739 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.50
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-ser248 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown