CLSTN1 p.Pro276=
c.828G>A · rs35261177 · VCV782355
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.77%, 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 -11 | GERP -4.7 |
| Overall | ||
| CADD | 0.078 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.77%
African / African-American · 1,325/75,052 alleles
Filtering AF
1.69%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.65%
Overall
0.11%
1,774/1,614,110 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.77% | 57 |
| Admixed American | 0.192% | 522 |
| Remaining individualsnot grpmax-eligible | 0.17% | 590 |
| Middle Eastern | 0.165% | 606 |
| Ashkenazi Jewishnot grpmax-eligible | 0.155% | 643 |
| European (non-Finnish) | 0.0136% | 7,375 |
| South Asian | 0.0121% | 8,280 |
| East Asian | 0.00223% | 44,890 |
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
- CLSTN1
- Protein
- p.Pro276=
- Coding
- c.828G>A
- MANE Select
- NM_001009566
- dbSNP
- rs35261177
- Type
- single nucleotide variant
- Location
- chr1:9749618 (GRCh38)
- Gene constraint
- LOEUF 0.341 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.63
Similar variants
- CLSTN1 p.Pro276Leu Uncertain significance ★ ⚠ same residue
- CLSTN1 p.Phe70Tyr Benign ★★ same type
- CLSTN1 p.Val109Ile Likely benign ★★ same type
- CLSTN1 p.Ala161Thr Uncertain significance ★ ⚠ same type
- CLSTN1 p.Ala161Val Uncertain significance ★ ⚠ same type
- CLSTN1 p.Ala540Val Uncertain significance ★ ⚠ same type
- CLSTN1 p.Ala550Ser Uncertain significance ★ ⚠ same type
- CLSTN1 p.Ala550Val 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/clstn1-p-pro276 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown