PDCD4 p.Glu34=
c.102G>A · rs140217953 · VCV747235
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.303%, afr)
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 2.3 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 9.85 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.303%
African / African-American · 227/75,020 alleles
Filtering AF
0.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.258%
Overall
0.0169%
272/1,613,442 alleles · rare
exomes 144/1,461,216 · genomes 128/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.303% | 330 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,499 |
| Admixed American | 0.025% | 4,000 |
| Middle Eastern | 0.0165% | 6,060 |
| South Asian | 0.0011% | 91,070 |
| European (non-Finnish) | 0.000254% | 393,147 |
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
- PDCD4
- Protein
- p.Glu34=
- Coding
- c.102G>A
- MANE Select
- NM_014456
- dbSNP
- rs140217953
- Type
- single nucleotide variant
- Location
- chr10:110881291 (GRCh38)
- Gene constraint
- LOEUF 1.671 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.03 · 11 PDB
- Residue 34
- the 'disordered' region
Similar variants
- PDCD4 p.Ala118Val Uncertain significance ★ ⚠ same type
- PDCD4 p.Ala84Thr Uncertain significance ★ ⚠ same type
- PDCD4 p.Arg310Cys Uncertain significance ★ ⚠ same type
- PDCD4 p.Arg428Trp Uncertain significance ★ ⚠ same type
- PDCD4 p.Arg61Thr Uncertain significance ★ ⚠ same type
- PDCD4 p.Arg69Trp Uncertain significance ★ ⚠ same type
- PDCD4 p.Asn410Ser Uncertain significance ★ ⚠ same type
- PDCD4 p.Asp144His 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/pdcd4-p-glu34 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown