CLMN p.Glu5=
c.15G>A · rs80288032 · VCV3060268
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 48.1%, eas) — too common for a highly-penetrant pathogenic allele
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 -1.8 | GERP -2.7 |
| Overall | ||
| CADD | 9.569 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
48.1%
East Asian · 20,237/42,088 alleles
Filtering AF
47.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 47.3%
Overall
5.02%
79,638/1,586,874 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 48.1% | 2 |
| Admixed American | 21.6% | 5 |
| South Asian | 13.7% | 7 |
| African / African-American | 11.8% | 8 |
| Remaining individualsnot grpmax-eligible | 6.48% | 15 |
| Ashkenazi Jewishnot grpmax-eligible | 2.59% | 39 |
| Middle Eastern | 2.05% | 49 |
| Finnishnot grpmax-eligible | 2.04% | 49 |
| European (non-Finnish) | 1.7% | 59 |
| Amishnot grpmax-eligible | 0.556% | 180 |
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.Glu5=
- Coding
- c.15G>A
- MANE Select
- NM_024734
- dbSNP
- rs80288032
- Type
- single nucleotide variant
- Location
- chr14:95319778 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.84
- Residue 5
- the 'actin-binding' region
Disease context
CLMN-related disorder
Similar variants
- CLMN c.608+7C>T Likely benign same condition
- CLMN p.Ala207= 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.Pro261= Likely benign same condition
- CLMN p.Pro850= Likely benign same condition
- CLMN p.Ser154= 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-glu5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown