ANKH p.His9=
c.27C>T · rs199583793 · VCV281904
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00534%, 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 6.1 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 13.85 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
European (non-Finnish) · 63/1,179,632 alleles
Filtering AF
0.00427%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00388%
Overall
0.00415%
67/1,613,228 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00534% | 18,724 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,810 |
| African / African-American | 0.00133% | 74,918 |
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.His9=
- Coding
- c.27C>T
- MANE Select
- NM_054027
- dbSNP
- rs199583793
- Type
- single nucleotide variant
- Location
- chr5:14871421 (GRCh38)
- Gene constraint
- LOEUF 0.463 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 84.57
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-his9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown