ARCN1 p.Val489=
c.1467A>G · rs144108474 · VCV718667
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.17%, 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 0.48 | GERP -1.6, phastCons 0.8 |
| Overall | ||
| CADD | 5.873 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.17%
East Asian · 522/44,696 alleles
Filtering AF
1.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.05%
Overall
0.0912%
1,471/1,612,336 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.17% | 86 |
| South Asian | 0.672% | 149 |
| Remaining individualsnot grpmax-eligible | 0.173% | 578 |
| Finnishnot grpmax-eligible | 0.139% | 719 |
| Ashkenazi Jewishnot grpmax-eligible | 0.132% | 758 |
| Middle Eastern | 0.033% | 3,028 |
| Admixed American | 0.0167% | 5,976 |
| European (non-Finnish) | 0.00763% | 13,103 |
| African / African-American | 0.00133% | 74,942 |
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.Val489=
- Coding
- c.1467A>G
- MANE Select
- NM_001655
- dbSNP
- rs144108474
- Type
- single nucleotide variant
- Location
- chr11:118600645 (GRCh38)
- Gene constraint
- LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 84.25
- Residue 489
- 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-val489 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown