PDCD11 p.Ser800=
c.2400G>A · rs752195699 · VCV2640805
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -6.7 | GERP -5.4 |
| Overall | ||
| CADD | 0.257 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.00154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00131%
Overall
0.00194%
31/1,601,314 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| South Asian | 0.00338% | 29,561 |
| European (non-Finnish) | 0.00221% | 45,153 |
| Admixed American | 0.00173% | 57,724 |
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
- PDCD11
- Protein
- p.Ser800=
- Coding
- c.2400G>A
- MANE Select
- NM_014976
- dbSNP
- rs752195699
- Type
- single nucleotide variant
- Location
- chr10:103421470 (GRCh38)
- Gene constraint
- LOEUF 0.573 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.40 · 1 PDB
Similar variants
- PDCD11 p.Ser800Leu Uncertain significance ★ ⚠ same residue
- PDCD11 p.Ala1131Gly Uncertain significance ★ ⚠ same type
- PDCD11 p.Ala1202Val Uncertain significance ★ ⚠ same type
- PDCD11 p.Ala1526Gly Uncertain significance ★ ⚠ same type
- PDCD11 p.Ala1526Thr Uncertain significance ★ ⚠ same type
- PDCD11 p.Ala1538Thr Uncertain significance ★ ⚠ same type
- PDCD11 p.Ala1594Val Uncertain significance ★ ⚠ same type
- PDCD11 p.Ala1605Glu 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/pdcd11-p-ser800 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown