CSPG4 p.Pro575=
c.1725T>C · rs372761533 · VCV2645577
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00935%, 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 -8.7 | GERP -3.1 |
| Overall | ||
| CADD | 0.061 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00935%
African / African-American · 7/74,868 alleles
Filtering AF
0.00438%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.00149%
24/1,611,308 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00935% | 10,695 |
| East Asian | 0.00223% | 44,884 |
| Admixed American | 0.00167% | 60,000 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,338 |
| European (non-Finnish) | 0.00119% | 84,274 |
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
- CSPG4
- Protein
- p.Pro575=
- Coding
- c.1725T>C
- MANE Select
- NM_001897
- dbSNP
- rs372761533
- Type
- single nucleotide variant
- Location
- chr15:75689340 (GRCh38)
- Gene constraint
- LOEUF 0.693 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.35 · 3 PDB
- Residue 575
- the 'globular or compact configuration stabilized by disulfide bonds' region; the 'neurite growth inhibition' region; the 'interaction with col6a2' region
Similar variants
- CSPG4 p.Arg2169Trp Uncertain significance ★★ ⚠ same type
- CSPG4 p.Arg1557His Likely benign ★★ same type
- CSPG4 p.Ser1882= Likely benign ★★ same type
- CSPG4 p.Thr305Met Benign ★★ ⚠ same type
- CSPG4 p.Ala1116Val Uncertain significance ★ ⚠ same type
- CSPG4 p.Ala1186Val Uncertain significance ★ ⚠ same type
- CSPG4 p.Ala1212Val Uncertain significance ★ ⚠ same type
- CSPG4 p.Ala121Thr 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/cspg4-p-pro575 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown