ARR3 p.Glu65Ter
c.193G>T · rs752013986 · VCV3234786
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 6 of 17 |
| Splicing | ||
| SpliceAI | Δ0.24 | acceptor loss · deltas |
| Constraint at this position | ||
| Conservation | phyloP 4.3 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 36.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ARR3
- Protein
- p.Glu65Ter
- Coding
- c.193G>T
- MANE Select
- NM_004312
- dbSNP
- rs752013986
- Type
- single nucleotide variant
- Location
- chrX:70276129 (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-glu65ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown