CRMP1 p.Pro528=
c.1584C>T · rs113703166 · VCV750183
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0843%, 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 -13 | GERP -4.6 |
| Overall | ||
| CADD | 0.069 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0843%
African / African-American · 62/73,578 alleles
Filtering AF
0.0675%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0614%
Overall
0.0116%
183/1,583,922 alleles · ultra-rare
exomes 153/1,431,666 · genomes 30/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0843% | 1,187 |
| Remaining individualsnot grpmax-eligible | 0.0213% | 4,703 |
| Middle Eastern | 0.0168% | 5,968 |
| South Asian | 0.00942% | 10,619 |
| European (non-Finnish) | 0.00824% | 12,141 |
| East Asian | 0.00232% | 43,052 |
| Admixed American | 0.00177% | 56,404 |
| Finnishnot grpmax-eligible | 0.00157% | 63,524 |
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
- CRMP1
- Protein
- p.Pro528=
- Coding
- c.1584C>T
- MANE Select
- NM_001014809
- dbSNP
- rs113703166
- Type
- single nucleotide variant
- Location
- chr4:5835954 (GRCh38)
- Gene constraint
- LOEUF 0.44 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 90.46 · 1 PDB
- Residue 528
- the 'disordered' region
Similar variants
- CRMP1 c.820+8A>G Benign ★★ same type
- CRMP1 c.964-8T>C Benign ★★ same type
- CRMP1 p.Ala357= Benign ★★ same type
- CRMP1 p.Gly261Arg Benign ★★ same type
- CRMP1 p.Val524= Benign ★★ same type
- CRMP1 c.381+2933T>C Uncertain significance ★ same type
- CRMP1 p.Ala174Val Uncertain significance ★ ⚠ same type
- CRMP1 p.Ala199Ser 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/crmp1-p-pro528 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown