IFT54 p.Lys295=
c.885G>A · rs12464423 · VCV1113790
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.065%, nfe)
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 2.1 | GERP 1.2, phastCons 0.054 |
| Overall | ||
| CADD | 6.064 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.065%
European (non-Finnish) · 699/1,075,718 alleles
Filtering AF
0.061%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0594%
Overall
0.0517%
729/1,409,386 alleles · ultra-rare
exomes 694/1,257,358 · genomes 35/152,028 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.065% | 1,539 |
| Remaining individualsnot grpmax-eligible | 0.0375% | 2,667 |
| African / African-American | 0.0116% | 8,638 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00479% | 20,858 |
| Finnishnot grpmax-eligible | 0.00178% | 56,060 |
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.Lys295=
- Coding
- c.885G>A
- MANE Select
- NM_015650
- dbSNP
- rs12464423
- Type
- single nucleotide variant
- Location
- chr2:238329312 (GRCh38)
- Structure
- AlphaFold pLDDT 61.95 · 2 PDB
- Residue 295
- the 'abolishes microtubules-binding when missing' region; a UniProt-annotated variant site (in); the 'disordered' region; the 'disc1-interaction domain' region
Similar variants
- IFT54 p.Lys295Asn Benign ★★ same residue
- TRAF3IP1 p.Lys295_Asn296delinsAsnThr Uncertain significance 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
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-lys295 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown