EIF6 p.Thr76=
c.228C>T · VCV3777808
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.128%, 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 1.8 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 8.766 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.128%
European (non-Finnish) · 1,516/1,180,010 alleles
Filtering AF
0.123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.121%
Overall
0.098%
1,582/1,613,968 alleles · rare
exomes 1,478/1,461,780 · genomes 104/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.128% | 778 |
| Remaining individualsnot grpmax-eligible | 0.0448% | 2,231 |
| Admixed American | 0.0233% | 4,284 |
| African / African-American | 0.0214% | 4,683 |
| Finnishnot grpmax-eligible | 0.00937% | 10,672 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| South Asian | 0.0011% | 91,042 |
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
- EIF6
- Protein
- p.Thr76=
- Coding
- c.228C>T
- MANE Select
- NM_002212
- Type
- single nucleotide variant
- Location
- chr20:35280795 (GRCh38)
- Gene constraint
- LOEUF 0.623 · pLI 0.65 (gnomAD)
- Structure
- AlphaFold pLDDT 91.12 · 48 PDB
Similar variants
- EIF6 p.Ala183Thr Uncertain significance ★ ⚠ same type
- EIF6 p.Arg100Gln Uncertain significance ★ ⚠ same type
- EIF6 p.Arg85Cys Uncertain significance ★ ⚠ same type
- EIF6 p.Arg85His Uncertain significance ★ ⚠ same type
- EIF6 p.Asn156Ser Uncertain significance ★ ⚠ same type
- EIF6 p.Asn9Thr Uncertain significance ★ same type
- EIF6 p.Asp144Asn Uncertain significance ★ ⚠ same type
- EIF6 p.Asp78Asn 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/eif6-p-thr76 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown