EARS2 p.Lys284=
c.852G>A · rs1965389692 · VCV3032219
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
EARS2-related disorder
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 0.37 | GERP -0.32, phastCons 0.99 |
| Overall | ||
| CADD | 6.999 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,036 alleles
Overall
6.2e-05%
1/1,612,878 alleles · very rare
exomes 1/1,460,556 · genomes 0/152,322 · 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
- EARS2
- Protein
- p.Lys284=
- Coding
- c.852G>A
- MANE Select
- NM_001083614
- dbSNP
- rs1965389692
- Type
- single nucleotide variant
- Location
- chr16:23534994 (GRCh38)
- Gene constraint
- LOEUF 1.138 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.84
- Residue 284
- a binding site
Disease context
EARS2-related disorder
Similar variants
- EARS2 p.Lys284Arg Uncertain significance ★ ⚠ same residue
- EARS2 p.Arg107His Pathogenic/Likely pathogenic ★★ ⚠ same condition
- EARS2 p.Arg108Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
- EARS2 p.Gly317Cys Pathogenic ★★ same condition
- EARS2 p.Arg107Cys Pathogenic ★ ⚠ same condition
- EARS2 p.Arg38Ter Likely pathogenic ★ same condition
- EARS2 p.Gln117Ter Likely pathogenic ★ same condition
- EARS2 p.Gln377Ter Likely pathogenic ★ same condition
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/ears2-p-lys284 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown