CLMN p.Ala207=
c.621G>A · rs139868659 · VCV3037511
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0652%, nfe)
Conditions
1
CLMN-related disorder
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 -10 | GERP -5.3 |
| Overall | ||
| CADD | 5.757 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0652%
European (non-Finnish) · 745/1,143,512 alleles
Filtering AF
0.0612%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0597%
Overall
0.0506%
771/1,523,016 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0652% | 1,535 |
| Remaining individualsnot grpmax-eligible | 0.0206% | 4,863 |
| Middle Eastern | 0.0177% | 5,642 |
| African / African-American | 0.00869% | 11,502 |
| East Asian | 0.0051% | 19,601 |
| Finnishnot grpmax-eligible | 0.00323% | 30,957 |
| South Asian | 0.00255% | 39,290 |
| Admixed American | 0.00245% | 40,864 |
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
- CLMN
- Protein
- p.Ala207=
- Coding
- c.621G>A
- MANE Select
- NM_024734
- dbSNP
- rs139868659
- Type
- single nucleotide variant
- Location
- chr14:95210867 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.84
- Residue 207
- the calponin-homology (ch) 2 domain; the 'actin-binding' region
Disease context
CLMN-related disorder
Similar variants
- CLMN p.Ala207Val Uncertain significance ★ ⚠ same residue
- CLMN c.608+7C>T Likely benign same condition
- CLMN p.Arg313= Likely benign same condition
- CLMN p.Arg517His Benign same condition
- CLMN p.Glu245= Likely benign same condition
- CLMN p.Glu5= Benign same condition
- CLMN p.Pro261= Likely benign same condition
- CLMN p.Pro850= Likely benign same condition
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/clmn-p-ala207 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown