SYNJ2 p.Pro1334=
c.4002G>A · rs3749847 · VCV2657081
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0373%, 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 -12 | GERP -3.5 |
| Overall | ||
| CADD | 0.095 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0373%
African / African-American · 28/75,038 alleles
Filtering AF
0.0265%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0229%
Overall
0.00675%
109/1,614,096 alleles · ultra-rare
exomes 92/1,461,800 · genomes 17/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0373% | 2,680 |
| East Asian | 0.0245% | 4,080 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,208 |
| Finnishnot grpmax-eligible | 0.0172% | 5,819 |
| South Asian | 0.00439% | 22,768 |
| European (non-Finnish) | 0.00347% | 28,781 |
| Admixed American | 0.00333% | 30,013 |
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
- SYNJ2
- Protein
- p.Pro1334=
- Coding
- c.4002G>A
- MANE Select
- NM_003898
- dbSNP
- rs3749847
- Type
- single nucleotide variant
- Location
- chr6:158095875 (GRCh38)
- Gene constraint
- LOEUF 0.968 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.47 · 1 PDB
- Residue 1334
- the 'disordered' region
Similar variants
- SYNJ2 p.Pro1334Ala Uncertain significance ★ ⚠ same residue
- SYNJ2 p.Asp1071Glu Uncertain significance ★★ ⚠ same type
- SYNJ2 p.Val420Ala Likely benign ★★ same type
- SYNJ2 p.Ala1072Thr Uncertain significance ★ ⚠ same type
- SYNJ2 p.Ala111Asp Uncertain significance ★ ⚠ same type
- SYNJ2 p.Ala1186Thr Uncertain significance ★ ⚠ same type
- SYNJ2 p.Ala1199Thr Uncertain significance ★ ⚠ same type
- SYNJ2 p.Ala1274Gly 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/synj2-p-pro1334 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown