CLSTN2 p.Asp613=
c.1839C>T · rs138834742 · VCV2654195
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.56%, 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 -5.9 | GERP -3.8 |
| Overall | ||
| CADD | 1.402 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.56%
African / African-American · 420/75,006 alleles
Filtering AF
0.516%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.498%
Overall
0.0356%
574/1,613,436 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.56% | 179 |
| Admixed American | 0.08% | 1,250 |
| Remaining individualsnot grpmax-eligible | 0.0544% | 1,837 |
| European (non-Finnish) | 0.00568% | 17,606 |
| South Asian | 0.00439% | 22,759 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,598 |
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
- CLSTN2
- Protein
- p.Asp613=
- Coding
- c.1839C>T
- MANE Select
- NM_022131
- dbSNP
- rs138834742
- Type
- single nucleotide variant
- Location
- chr3:140558655 (GRCh38)
- Gene constraint
- LOEUF 0.578 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.46
Similar variants
- CLSTN2 p.Asp613Glu Uncertain significance ★ ⚠ same residue
- CLSTN2 c.233-8T>G Benign ★★ same type
- CLSTN2 p.Gly776= Benign ★★ same type
- CLSTN2 p.Ile124= Benign ★★ same type
- CLSTN2 p.Ile306Asn Likely benign ★★ ⚠ same type
- CLSTN2 p.Ala131Thr Uncertain significance ★ ⚠ same type
- CLSTN2 p.Ala137Asp Uncertain significance ★ ⚠ same type
- CLSTN2 p.Ala243Thr Uncertain significance ★ ⚠ 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/clstn2-p-asp613 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown