CLMP p.Leu151=
c.453G>A · rs112659755 · VCV784224
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.13%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -0.93, phastCons 1 |
| Overall | ||
| CADD | 11.61 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.13%
African / African-American · 2,345/75,038 alleles
Filtering AF
3.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.98%
Overall
0.177%
2,861/1,613,988 alleles · low-frequency
exomes 1,475/1,461,698 · genomes 1,386/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.13% | 32 |
| Admixed American | 0.278% | 359 |
| Middle Eastern | 0.254% | 394 |
| Remaining individualsnot grpmax-eligible | 0.218% | 459 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0405% | 2,467 |
| European (non-Finnish) | 0.0156% | 6,413 |
| South Asian | 0.0022% | 45,535 |
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
- CLMP
- Protein
- p.Leu151=
- Coding
- c.453G>A
- MANE Select
- NM_024769
- dbSNP
- rs112659755
- Type
- single nucleotide variant
- Location
- chr11:123083783 (GRCh38)
- Gene constraint
- LOEUF 0.792 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.52
- Residue 151
- the ig-like c2-type 2 domain
Similar variants
- CLMP p.Arg222Ter Pathogenic ★★ same type
- CLMP p.Asp55Asn Benign ★★ same type
- CLMP p.Gly337= Benign ★★ same type
- CLMP p.Ser296= Benign ★★ same type
- CLMP c.28+1G>A Likely pathogenic ★ same type
- CLMP p.Arg192Ter Likely pathogenic ★ same type
- CLMP p.Arg82Ter Likely pathogenic ★ same type
- CLMP p.Gly141Ter Pathogenic ★ 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/clmp-p-leu151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown