ARR3 p.Pro305=
c.915G>A · rs144619692 · VCV2660809
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.023%, mid)
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 -1.7 | GERP -3.9 |
| Overall | ||
| CADD | 0.796 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.023%
Middle Eastern · 1/4,353 alleles
Filtering AF
0.0121%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00957%
Overall
0.00356%
43/1,208,802 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.023% | 4,353 |
| South Asian | 0.0212% | 4,723 |
| Remaining individualsnot grpmax-eligible | 0.00631% | 15,860 |
| East Asian | 0.00593% | 16,874 |
| African / African-American | 0.00526% | 19,027 |
| European (non-Finnish) | 0.00235% | 42,589 |
| Finnishnot grpmax-eligible | 0.00215% | 46,519 |
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.Pro305=
- Coding
- c.915G>A
- MANE Select
- NM_004312
- dbSNP
- rs144619692
- Type
- single nucleotide variant
- Location
- chrX:70280204 (GRCh38)
- Structure
- AlphaFold pLDDT 87.37
- Residue 305
- a UniProt-annotated variant site (in myp26; uncertain significance)
Similar variants
- ARR3 p.Pro305Leu Likely benign ★ ⚠ same residue
- 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
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-pro305 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown