ARR3 p.Ser9=
c.27C>T · rs3818862 · VCV3056529
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 35.4%, eas) — too common for a highly-penetrant pathogenic allele
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 0.1 | GERP -0.83, phastCons 0.94 |
| Overall | ||
| CADD | 11.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
35.4%
East Asian · 11,878/33,531 alleles
Filtering AF
34.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 34.7%
Overall
7.96%
95,738/1,203,359 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 35.4% | 3 |
| South Asian | 21% | 5 |
| Amishnot grpmax-eligible | 15.7% | 6 |
| African / African-American | 12.2% | 8 |
| Ashkenazi Jewishnot grpmax-eligible | 10.4% | 10 |
| Admixed American | 10.2% | 10 |
| Remaining individualsnot grpmax-eligible | 9.98% | 10 |
| Middle Eastern | 6.56% | 15 |
| European (non-Finnish) | 5.71% | 17 |
| Finnishnot grpmax-eligible | 5.04% | 20 |
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
- ARR3
- Protein
- p.Ser9=
- Coding
- c.27C>T
- MANE Select
- NM_004312
- dbSNP
- rs3818862
- Type
- single nucleotide variant
- Location
- chrX:70269680 (GRCh38)
- Structure
- AlphaFold pLDDT 87.37
Similar variants
- ARR3 c.767+1G>A Pathogenic/Likely pathogenic ★★ same type
- ARR3 p.Arg72Ter Pathogenic/Likely pathogenic ★★ same type
- ARR3 p.Val82Met Uncertain significance ★★ ⚠ same type
- ARR3 c.346-4C>T Benign/Likely benign ★★ same type
- ARR3 p.Arg282Gln Likely benign ★★ ⚠ same type
- ARR3 p.His205= Likely benign ★★ same type
- ARR3 p.His207= Benign/Likely benign ★★ same type
- ARR3 p.Ile217Val Likely benign ★★ 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/arr3-p-ser9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown