CLMN p.Thr39=
c.117A>G · rs116124564 · VCV2644496
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.165%, afr)
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 -1.3 | GERP -5 |
| Overall | ||
| CADD | 2.505 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.165%
African / African-American · 124/75,064 alleles
Filtering AF
0.142%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.133%
Overall
0.00911%
147/1,614,238 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.165% | 605 |
| Middle Eastern | 0.0495% | 2,021 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,683 |
| Admixed American | 0.00666% | 15,009 |
| South Asian | 0.00439% | 22,771 |
| European (non-Finnish) | 8.47e-05% | 1,180,034 |
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
- CLMN
- Protein
- p.Thr39=
- Coding
- c.117A>G
- MANE Select
- NM_024734
- dbSNP
- rs116124564
- Type
- single nucleotide variant
- Location
- chr14:95230099 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.84
- Residue 39
- the calponin-homology (ch) 1 domain; the 'actin-binding' region
Similar variants
- CLMN c.2511+10C>T Benign ★★ same type
- CLMN c.886-4G>T Likely benign ★★ same type
- CLMN p.Asp592= Benign ★★ same type
- CLMN p.Glu276Lys Likely benign ★★ same type
- CLMN p.Glu357Lys Benign ★★ same type
- CLMN p.Glu771Ala Likely benign ★★ same type
- CLMN p.His518= Benign ★★ same type
- CLMN p.Ile900Phe Benign ★★ 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/clmn-p-thr39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown