ARR3 p.Pro173=
c.519G>A · VCV4951299
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, 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 0.008 | GERP -3.3, phastCons 0.001 |
| Overall | ||
| CADD | 5.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 6/33,764 alleles
Filtering AF
0.00766%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00527%
Overall
0.000909%
11/1,210,009 alleles · ultra-rare
exomes 9/1,097,945 · genomes 2/112,064 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0178% | 5,627 |
| African / African-American | 0.00699% | 14,304 |
| European (non-Finnish) | 0.000112% | 895,151 |
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.Pro173=
- Coding
- c.519G>A
- MANE Select
- NM_004312
- Type
- single nucleotide variant
- Location
- chrX:70277439 (GRCh38)
- Structure
- AlphaFold pLDDT 87.37
- Residue 173
- a UniProt-annotated variant site (in myp26; uncertain significance)
Similar variants
- ARR3 p.Pro173Leu 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-pro173 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown