CLMN p.Ser704=
c.2112C>T · rs140829875 · VCV3041361
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.22%, 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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.2 | GERP -4.8 |
| Overall | ||
| CADD | 0.557 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.22%
Middle Eastern · 13/5,918 alleles
Filtering AF
0.13%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.103%
Overall
0.0323%
521/1,613,800 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.22% | 455 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0541% | 1,850 |
| Remaining individualsnot grpmax-eligible | 0.0416% | 2,403 |
| European (non-Finnish) | 0.0353% | 2,837 |
| South Asian | 0.0286% | 3,503 |
| Admixed American | 0.0267% | 3,751 |
| African / African-American | 0.00933% | 10,717 |
| Finnishnot grpmax-eligible | 0.00157% | 63,890 |
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.Ser704=
- Coding
- c.2112C>T
- MANE Select
- NM_024734
- dbSNP
- rs140829875
- Type
- single nucleotide variant
- Location
- chr14:95203237 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.84
- Residue 704
- 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-ser704 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown