CLMP p.Asp321=
c.963C>T · rs199985664 · VCV3044307
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, amr)
Conditions
1
CLMP-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 -1.4 | GERP -3.5, phastCons 0.001 |
| Overall | ||
| CADD | 6.204 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
Admixed American · 12/60,030 alleles
Filtering AF
0.0115%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00898%
Overall
0.00353%
57/1,614,232 alleles · ultra-rare
exomes 48/1,461,888 · genomes 9/152,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.02% | 5,003 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| African / African-American | 0.00666% | 15,012 |
| European (non-Finnish) | 0.00288% | 34,707 |
| South Asian | 0.0011% | 91,086 |
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.Asp321=
- Coding
- c.963C>T
- MANE Select
- NM_024769
- dbSNP
- rs199985664
- Type
- single nucleotide variant
- Location
- chr11:123073633 (GRCh38)
- Gene constraint
- LOEUF 0.792 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.52
- Residue 321
- the 'disordered' region
Disease context
CLMP-related disorder
Similar variants
- CLMP p.Pro100Ser Likely benign same condition
- CLMP p.Arg222Ter Pathogenic ★★ same type
- CLMP p.Asp55Asn Benign ★★ same type
- CLMP p.Gly337= Benign ★★ same type
- CLMP p.Leu151= 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
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-asp321 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown