PDS5B p.Asp1202=
c.3606C>T · rs41292175 · VCV790868
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.498%, 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 0.45 | GERP -0.055, phastCons 0.99 |
| Overall | ||
| CADD | 11.13 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.498%
European (non-Finnish) · 5,762/1,157,092 alleles
Filtering AF
0.487%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.483%
Overall
0.394%
6,234/1,583,328 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.498% | 201 |
| Remaining individualsnot grpmax-eligible | 0.259% | 386 |
| Middle Eastern | 0.167% | 598 |
| Finnishnot grpmax-eligible | 0.147% | 682 |
| Ashkenazi Jewishnot grpmax-eligible | 0.126% | 791 |
| African / African-American | 0.104% | 964 |
| Admixed American | 0.0647% | 1,546 |
| South Asian | 0.0634% | 1,576 |
| East Asian | 0.00454% | 22,044 |
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
- PDS5B
- Protein
- p.Asp1202=
- Coding
- c.3606C>T
- MANE Select
- NM_015032
- dbSNP
- rs41292175
- Type
- single nucleotide variant
- Location
- chr13:32764576 (GRCh38)
- Gene constraint
- LOEUF 0.498 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 80.85 · 1 PDB
- Residue 1202
- the 'disordered' region
Similar variants
- PDS5B p.Asp1202His Uncertain significance ★ ⚠ same residue
- PDS5B p.Asn284= Benign ★★ same type
- PDS5B c.625-1G>C Uncertain significance ★ same type
- PDS5B p.Ala1399Gly Uncertain significance ★ ⚠ same type
- PDS5B p.Ala1399Thr Uncertain significance ★ ⚠ same type
- PDS5B p.Ala520Val Uncertain significance ★ ⚠ same type
- PDS5B p.Ala576Ser Uncertain significance ★ ⚠ same type
- PDS5B p.Ala576Val 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/pds5b-p-asp1202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown