ARR3 p.Leu80=
c.238C>T · VCV4951294
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0019%, nfe)
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 -0.07 | GERP -4.5 |
| Overall | ||
| CADD | 6.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0019%
European (non-Finnish) · 17/895,160 alleles
Filtering AF
0.00116%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000946%
Overall
0.0014%
17/1,209,966 alleles · very rare
exomes 13/1,098,040 · genomes 4/111,926 · joint denominator
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.Leu80=
- Coding
- c.238C>T
- MANE Select
- NM_004312
- Type
- single nucleotide variant
- Location
- chrX:70276174 (GRCh38)
- Structure
- AlphaFold pLDDT 87.37
- Residue 80
- a UniProt-annotated variant site (in myp26; uncertain significance)
Similar variants
- ARR3 p.Leu80Pro Pathogenic ⚠ 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-leu80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown