ARCN1 p.Asp289=
c.867C>T · rs371011063 · VCV731837
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.18%, eas)
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 -0.076 | GERP -1.7, phastCons 0.87 |
| Overall | ||
| CADD | 10.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.18%
East Asian · 81/44,882 alleles
Filtering AF
0.149%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.137%
Overall
0.00818%
132/1,613,844 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.18% | 554 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,166 |
| Admixed American | 0.00667% | 15,001 |
| South Asian | 0.00659% | 15,180 |
| European (non-Finnish) | 0.00212% | 47,192 |
| African / African-American | 0.00133% | 75,016 |
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
- ARCN1
- Protein
- p.Asp289=
- Coding
- c.867C>T
- MANE Select
- NM_001655
- dbSNP
- rs371011063
- Type
- single nucleotide variant
- Location
- chr11:118590389 (GRCh38)
- Gene constraint
- LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 84.25
- Residue 289
- the mhd domain
Similar variants
- ARCN1 c.654-15A>G Pathogenic/Likely pathogenic ★★ same type
- ARCN1 p.Arg170Ter Pathogenic ★★ same type
- ARCN1 p.Arg312Ter Pathogenic ★★ same type
- ARCN1 p.Arg435Ter Pathogenic/Likely pathogenic ★★ same type
- ARCN1 p.Ala169Val Uncertain significance ★★ ⚠ same type
- ARCN1 p.Arg160His Uncertain significance ★★ ⚠ same type
- ARCN1 p.Arg161His Uncertain significance ★★ ⚠ same type
- ARCN1 p.Arg314His 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/arcn1-p-asp289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown