CSMD2 p.Pro1506=
c.4518G>T · rs747379869 · VCV2638629
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.115%, 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 -15 | GERP -5.2 |
| Overall | ||
| CADD | 0.161 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.115%
Middle Eastern · 7/6,082 alleles
Filtering AF
0.0561%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.05%
Overall
0.00985%
159/1,614,002 alleles · rare
exomes 125/1,461,856 · genomes 34/152,146 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.115% | 869 |
| Admixed American | 0.0733% | 1,364 |
| South Asian | 0.0329% | 3,036 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,207 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,802 |
| European (non-Finnish) | 0.00517% | 19,344 |
| East Asian | 0.00445% | 22,448 |
| Finnishnot grpmax-eligible | 0.00156% | 64,034 |
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
- CSMD2
- Protein
- p.Pro1506=
- Coding
- c.4518G>T
- MANE Select
- NM_001281956
- dbSNP
- rs747379869
- Type
- single nucleotide variant
- Location
- chr1:33652391 (GRCh38)
- Gene constraint
- LOEUF 0.364 · pLI 1.00 (gnomAD)
- Residue 1506
- the cub 9 domain
Similar variants
- CSMD2 p.Ser3015= Benign ★★ same type
- CSMD2 c.404+2T>A Uncertain significance ★ same type
- CSMD2 c.6344-398G>T Uncertain significance ★ same type
- CSMD2 c.6344-422A>G Uncertain significance ★ same type
- CSMD2 c.6344-423T>C Uncertain significance ★ same type
- CSMD2 c.6344-429G>A Uncertain significance ★ same type
- CSMD2 c.6344-435G>A Uncertain significance ★ same type
- CSMD2 c.6344-437C>G 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/csmd2-p-pro1506 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown