ARR3 p.Tyr110Ter
c.330C>A · rs2520927898 · VCV3032603
Likely pathogenic
No assertion criteria
Classification
Likely pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
ARR3-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 6 of 17 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.22 | GERP -1.7, phastCons 0.41 |
| Overall | ||
| CADD | 34.0 | 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.Tyr110Ter
- Coding
- c.330C>A
- MANE Select
- NM_004312
- dbSNP
- rs2520927898
- Type
- single nucleotide variant
- Location
- chrX:70276266 (GRCh38)
- Structure
- AlphaFold pLDDT 87.37
- Residue 110
- a UniProt-annotated variant site (in myp26; uncertain significance)
Disease context
ARR3-related disorder
Similar variants
- ARR3 p.Arg72Ter Pathogenic/Likely pathogenic ★★ same condition
- ARR3 c.8+1G>T Likely pathogenic ★ same condition
- ARR3 c.905+2T>G Likely pathogenic ★ same condition
- ARR3 p.Ala382Asp Uncertain significance ⚠ same condition
- ARR3 p.Gly306fs Likely pathogenic same condition
- ARR3 c.767+1G>A Pathogenic/Likely pathogenic ★★ same type
- ARR3 p.Val82Met Uncertain significance ★★ ⚠ same type
- ARR3 c.346-4C>T 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-tyr110ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown