ARR3 p.Phe368=
c.1104T>C · VCV3778225
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00249%, 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 -1.2 | GERP -3.5 |
| Overall | ||
| CADD | 0.742 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00249%
European (non-Finnish) · 22/882,996 alleles
Filtering AF
0.00163%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00139%
Overall
0.00214%
23/1,074,470 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00249% | 40,136 |
| Remaining individualsnot grpmax-eligible | 0.00214% | 46,724 |
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.Phe368=
- Coding
- c.1104T>C
- MANE Select
- NM_004312
- Type
- single nucleotide variant
- Location
- chrX:70281703 (GRCh38)
- Structure
- AlphaFold pLDDT 87.37
- Residue 368
- a UniProt-annotated variant site (in myp26; uncertain significance)
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-phe368 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown