ELF3 p.Ser68=
c.204G>A · VCV3389488
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00445%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.37 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.7 | GERP -4.5 |
| Overall | ||
| CADD | 9.146 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00445%
East Asian · 2/44,902 alleles
Filtering AF
0.00164%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00142%
Overall
0.00198%
32/1,614,002 alleles · very rare
exomes 30/1,461,782 · genomes 2/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00445% | 22,451 |
| European (non-Finnish) | 0.00237% | 42,145 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| South Asian | 0.0011% | 91,088 |
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
- ELF3
- Protein
- p.Ser68=
- Coding
- c.204G>A
- MANE Select
- NM_004433
- Type
- single nucleotide variant
- Location
- chr1:202011997 (GRCh38)
- Gene constraint
- LOEUF 0.678 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.32 · 1 PDB
- Residue 68
- the pnt domain
Similar variants
- ELF3 p.Asn104= Benign ★★ same type
- ELF3 p.Arg205Trp Uncertain significance ★ ⚠ same type
- ELF3 p.Arg233Cys Uncertain significance ★ ⚠ same type
- ELF3 p.Arg307His Uncertain significance ★ ⚠ same type
- ELF3 p.Arg370Gln Uncertain significance ★ ⚠ same type
- ELF3 p.Arg370Trp Uncertain significance ★ ⚠ same type
- ELF3 p.Asp220Tyr Uncertain significance ★ ⚠ same type
- ELF3 p.Asp234Asn Uncertain significance ★ ⚠ 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/elf3-p-ser68 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown