CLMN p.Ser154=
c.462C>T · VCV3351689
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0823%, mid)
Conditions
1
CLMN-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.39 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.3 | GERP 0.024, phastCons 1 |
| Overall | ||
| CADD | 6.917 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0823%
Middle Eastern · 5/6,078 alleles
Filtering AF
0.0323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.021%
Overall
0.000868%
14/1,612,398 alleles · ultra-rare
exomes 13/1,460,236 · genomes 1/152,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0823% | 1,216 |
| South Asian | 0.00661% | 15,133 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,404 |
| European (non-Finnish) | 0.00017% | 589,769 |
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.Ser154=
- Coding
- c.462C>T
- MANE Select
- NM_024734
- Type
- single nucleotide variant
- Location
- chr14:95213365 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.84
- Residue 154
- the 'actin-binding' region; the 'disordered' 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.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-ser154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown