IFT57 p.Arg21=
c.63T>C · rs149187872 · VCV1579491
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, afr)
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 -0.38 | GERP -5.3, phastCons 0.004 |
| Overall | ||
| CADD | 8.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
African / African-American · 20/74,894 alleles
Filtering AF
0.0177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0147%
Overall
0.0013%
21/1,613,828 alleles · ultra-rare
exomes 13/1,461,726 · genomes 8/152,102 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0267% | 3,745 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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
- IFT57
- Protein
- p.Arg21=
- Coding
- c.63T>C
- MANE Select
- NM_018010
- dbSNP
- rs149187872
- Type
- single nucleotide variant
- Location
- chr3:108222260 (GRCh38)
- Gene constraint
- LOEUF 1.425 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.92
Similar variants
- IFT57 c.585+3A>G Likely pathogenic ★★ same type
- IFT57 c.981+4A>G Uncertain significance ★★ same type
- IFT57 p.Ala155Thr Uncertain significance ★★ ⚠ same type
- IFT57 p.Ala37Val Uncertain significance ★★ ⚠ same type
- IFT57 p.Arg245Cys Uncertain significance ★★ ⚠ same type
- IFT57 p.Asp110Ala Uncertain significance ★★ ⚠ same type
- IFT57 p.Asp219His Uncertain significance ★★ ⚠ same type
- IFT57 p.Asp228His Uncertain significance ★★ ⚠ same type
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/ift57-p-arg21 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown