ANKH p.Ile484=
c.1452C>T · rs374610746 · VCV2186551
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0428%, 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 -0.08 | GERP -1.8, phastCons 0.001 |
| Overall | ||
| CADD | 12.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0428%
South Asian · 39/91,080 alleles
Filtering AF
0.0322%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0284%
Overall
0.00582%
94/1,613,922 alleles · ultra-rare
exomes 89/1,461,846 · genomes 5/152,076 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0428% | 2,335 |
| East Asian | 0.00669% | 14,957 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
| European (non-Finnish) | 0.00415% | 24,081 |
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
- ANKH
- Protein
- p.Ile484=
- Coding
- c.1452C>T
- MANE Select
- NM_054027
- dbSNP
- rs374610746
- Type
- single nucleotide variant
- Location
- chr5:14711224 (GRCh38)
- Gene constraint
- LOEUF 0.463 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 84.57
- Residue 484
- the 'disordered' region
Similar variants
- ANKH c.1142-4A>G Pathogenic/Likely pathogenic ★★ same type
- ANKH c.96+5G>A Uncertain significance ★★ same type
- ANKH c.*3752G>A Uncertain significance ★★ same type
- ANKH p.Ala136Thr Uncertain significance ★★ ⚠ same type
- ANKH p.Ala201Thr Uncertain significance ★★ ⚠ same type
- ANKH p.Ala448Thr Uncertain significance ★★ same type
- ANKH p.Arg453Gln Uncertain significance ★★ ⚠ same type
- ANKH p.Asn306Asp 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/ankh-p-ile484 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown