EEF1D p.Thr575=
c.1725G>A · rs145499695 · VCV3040628
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.145%, afr)
Conditions
1
EEF1D-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.035 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.7 |
| Overall | ||
| CADD | 2.135 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.145%
African / African-American · 109/74,930 alleles
Filtering AF
0.123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.115%
Overall
0.00781%
126/1,613,344 alleles · rare
exomes 68/1,461,128 · genomes 58/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.145% | 687 |
| Middle Eastern | 0.0496% | 2,015 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,922 |
| Admixed American | 0.00167% | 59,966 |
| South Asian | 0.0011% | 91,068 |
| European (non-Finnish) | 0.000424% | 235,968 |
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
- EEF1D
- Protein
- p.Thr575=
- Coding
- c.1725G>A
- MANE Select
- NM_001130053
- dbSNP
- rs145499695
- Type
- single nucleotide variant
- Location
- chr8:143580192 (GRCh38)
- Gene constraint
- LOEUF 1.085 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.66 · 4 PDB
- Residue 575
- a UniProt-annotated variant site (in nedtchal; likely pathogenic)
Disease context
EEF1D-related disorder
Similar variants
- EEF1D p.Thr575Met Uncertain significance ★★ ⚠ same residue
- EEF1D p.Asp386Asn Uncertain significance ★★ ⚠ same condition
- EEF1D p.Arg292Ter Likely pathogenic ★ same condition
- EEF1D p.Gln610Ter Likely pathogenic ★ same condition
- EEF1D c.1288-10T>C Likely benign same condition
- EEF1D p.Ala35= Likely benign same condition
- EEF1D p.Ala549Ser Likely benign same condition
- EEF1D p.Ala578= Benign 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/eef1d-p-thr575 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown