AGRN p.Pro2000Leu
c.5999C>T · rs1304893940 · VCV3097139
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,559,930)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.238 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.8 | GERP 1.3, phastCons 1 |
| Regional constraint | o/e 1.02 | unconstrained · MANE · 8,500 bp · p 0.41 · regional, not allelic |
| Overall | ||
| CADD | 22.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,559,930). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- AGRN
- Protein
- p.Pro2000Leu
- Coding
- c.5999C>T
- MANE Select
- NM_198576
- dbSNP
- rs1304893940
- Type
- single nucleotide variant
- Location
- chr1:1054842 (GRCh38)
- Gene constraint
- LOEUF 0.73 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 69.79 · 1 PDB
- Residue 2000
- the laminin g-like 3 domain
Similar variants
- AGRN p.Pro2000Ser Uncertain significance ★★ same residue
- AGRN p.Pro2000= Likely benign ★ same residue
- AGRN p.Ala1012Thr Uncertain significance ★★ same condition
- AGRN p.Ala1056Thr Uncertain significance ★★ same condition
- AGRN p.Ala1304Thr Uncertain significance ★★ same condition
- AGRN p.Ala1325Gly Uncertain significance ★★ same condition
- AGRN p.Ala1372Thr Uncertain significance ★★ same condition
- AGRN p.Ala1737Val Uncertain significance ★★ same condition
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/agrn-p-pro2000leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown