IFT54 p.Ala613=
c.1839C>T · VCV4960794
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0201%, eas)
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 4.6 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 13.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0201%
East Asian · 9/44,880 alleles
Filtering AF
0.0104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00779%
Overall
0.000558%
9/1,612,804 alleles · ultra-rare
exomes 9/1,460,554 · genomes 0/152,250 · joint denominator
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
- IFT54
- Protein
- p.Ala613=
- Coding
- c.1839C>T
- MANE Select
- NM_015650
- Type
- single nucleotide variant
- Location
- chr2:238397608 (GRCh38)
- Structure
- AlphaFold pLDDT 61.95 · 2 PDB
- Residue 613
- the 'disc1-interaction domain' region
Similar variants
- TRAF3IP1 p.Ala613= Likely benign ★ same residue
- IFT54 c.1159+1G>C Likely pathogenic ★★ same type
- IFT54 c.988-1G>A Likely pathogenic ★★ same type
- IFT54 c.988-1G>C Likely pathogenic ★★ same type
- IFT54 p.Arg565Ter Pathogenic/Likely pathogenic ★★ same type
- IFT54 p.Trp572Ter Pathogenic/Likely pathogenic ★★ same type
- IFT54 c.1452-5T>G Uncertain significance ★★ same type
- IFT54 c.1910+3G>T 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/ift54-p-ala613 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown