IFT54 p.Val370=
c.1110G>A · rs570337103 · VCV1164767
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.475%, sas)
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 1.9 | GERP 0.1, phastCons 0.94 |
| Overall | ||
| CADD | 1.597 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.475%
South Asian · 419/88,268 alleles
Filtering AF
0.437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.422%
Overall
0.0275%
441/1,601,126 alleles · rare
exomes 415/1,448,824 · genomes 26/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.475% | 211 |
| Remaining individualsnot grpmax-eligible | 0.0226% | 4,423 |
| Middle Eastern | 0.0198% | 5,056 |
| Admixed American | 0.00522% | 19,170 |
| African / African-American | 0.00402% | 24,857 |
| European (non-Finnish) | 8.51e-05% | 1,174,929 |
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.Val370=
- Coding
- c.1110G>A
- MANE Select
- NM_015650
- dbSNP
- rs570337103
- Type
- single nucleotide variant
- Location
- chr2:238338408 (GRCh38)
- Structure
- AlphaFold pLDDT 61.95 · 2 PDB
- Residue 370
- the 'disordered' region; the 'disc1-interaction domain' region
Similar variants
- 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
- IFT54 p.Ala513Val 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-val370 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown