ANKH p.Ser239Arg
c.717C>A · VCV3766252
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.6548 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
AlphaMissense, SaProt · REVEL no call
Computational evidence
| Protein change | ||
| AlphaMissense | 0.6548 | likely pathogenic |
|---|---|---|
| REVEL | 0.624 | indeterminate |
| SaProt | LLR -6.29 | tolerated |
| ⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP -1.2, phastCons 1 |
| Regional constraint | o/e 0.61 | unconstrained · MANE · 160 kb · p 1.1e-21 · regional, not allelic |
| Overall | ||
| CADD | 18.62 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ANKH
- Protein
- p.Ser239Arg
- Coding
- c.717C>A
- MANE Select
- NM_054027
- Type
- single nucleotide variant
- Location
- chr5:14749277 (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-ser239arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown