CSPG4 p.Arg702=
c.2106C>T · rs144158910 · VCV2645574
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.11%, 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 -5.2 | GERP -3.1 |
| Overall | ||
| CADD | 0.154 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.11%
Middle Eastern · 181/5,814 alleles
Filtering AF
2.74%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.6%
Overall
0.816%
13,163/1,612,524 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 3.11% | 32 |
| Finnishnot grpmax-eligible | 1.26% | 80 |
| Ashkenazi Jewishnot grpmax-eligible | 1.19% | 84 |
| Remaining individualsnot grpmax-eligible | 0.935% | 107 |
| European (non-Finnish) | 0.84% | 119 |
| South Asian | 0.808% | 124 |
| Admixed American | 0.773% | 129 |
| Amishnot grpmax-eligible | 0.22% | 455 |
| African / African-American | 0.169% | 591 |
| East Asian | 0.029% | 3,453 |
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.Arg702=
- Coding
- c.2106C>T
- MANE Select
- NM_001897
- dbSNP
- rs144158910
- Type
- single nucleotide variant
- Location
- chr15:75688959 (GRCh38)
- Gene constraint
- LOEUF 0.693 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.35 · 3 PDB
- Residue 702
- the 'interaction with col6a2' region; the 'interaction with col5a1' region
Similar variants
- CSPG4 p.Arg702His Uncertain significance ★ ⚠ same residue
- 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
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-arg702 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown