SRPK2 p.Pro25=
c.75G>A · rs56318802 · VCV782848
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 6.25%, eas) — too common for a highly-penetrant pathogenic allele
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 0.61 | GERP 0.56, phastCons 1 |
| Overall | ||
| CADD | 14.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.25%
East Asian · 2,688/43,018 alleles
Filtering AF
6.05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.97%
Overall
0.287%
4,530/1,579,058 alleles · common
exomes 4,062/1,426,870 · genomes 468/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 6.25% | 16 |
| South Asian | 1.28% | 78 |
| Remaining individualsnot grpmax-eligible | 0.834% | 120 |
| Middle Eastern | 0.0832% | 1,202 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0794% | 1,259 |
| Admixed American | 0.0631% | 1,585 |
| African / African-American | 0.0485% | 2,060 |
| European (non-Finnish) | 0.0107% | 9,372 |
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
- SRPK2
- Protein
- p.Pro25=
- Coding
- c.75G>A
- MANE Select
- NM_182692
- dbSNP
- rs56318802
- Type
- single nucleotide variant
- Location
- chr7:105203782 (GRCh38)
- Gene constraint
- LOEUF 0.347 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.62 · 3 PDB
- Residue 25
- the 'disordered' region
Similar variants
- SRPK2 p.Pro25Leu Uncertain significance ★ ⚠ same residue
- SRPK2 p.Lys270Gln Uncertain significance ★★ ⚠ same type
- SRPK2 p.Gly114= Benign ★★ same type
- SRPK2 p.Ile370= Benign ★★ same type
- SRPK2 p.Pro450= Benign ★★ same type
- SRPK2 c.514+1G>A Uncertain significance ★ same type
- SRPK2 p.Ala382Glu Uncertain significance ★ ⚠ same type
- SRPK2 p.Ala72Val 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/srpk2-p-pro25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown