PDCD10 p.Lys65=
c.195A>G · rs147071945 · VCV1783379
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0147%, afr)
Conditions
1
Inborn genetic diseases
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 4.3 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 11.72 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0147%
African / African-American · 11/75,016 alleles
Filtering AF
0.00814%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00633%
Overall
0.000683%
11/1,611,386 alleles · ultra-rare
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
- PDCD10
- Protein
- p.Lys65=
- Coding
- c.195A>G
- MANE Select
- NM_007217
- dbSNP
- rs147071945
- Type
- single nucleotide variant
- Location
- chr3:167697082 (GRCh38)
- Gene constraint
- LOEUF 0.924 · pLI 0.64 (gnomAD)
- Structure
- AlphaFold pLDDT 90.82 · 10 PDB
- Residue 65
- an α-helix
Similar variants
- PDCD10 p.Lys65Gln Uncertain significance ★ ⚠ same residue
- PDCD10 p.Asn104Ser Uncertain significance ★★ ⚠ same condition
- PDCD10 p.Leu44Arg Uncertain significance ★★ ⚠ same condition
- PDCD10 p.Phe76Val Uncertain significance ★★ ⚠ same condition
- PDCD10 p.Tyr27Cys Uncertain significance ★★ ⚠ same condition
- PDCD10 p.Ala46= Likely benign ★★ same condition
- PDCD10 p.Phe127= Likely benign ★★ same condition
- PDCD10 p.Val72Leu Benign/Likely 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/pdcd10-p-lys65 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown