RELN p.Ser3340=
c.10020G>A · rs760919496 · VCV475943
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, sas)
Conditions
2
familial temporal lobe epilepsy 7
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 -8.3 | GERP -3.9 |
| Overall | ||
| CADD | 0.156 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
South Asian · 15/91,084 alleles
Filtering AF
0.0101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00811%
Overall
0.00291%
47/1,613,882 alleles · ultra-rare
exomes 43/1,461,672 · genomes 4/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0165% | 6,072 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,411 |
| East Asian | 0.00668% | 14,965 |
| Admixed American | 0.005% | 20,002 |
| European (non-Finnish) | 0.0017% | 58,994 |
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
- RELN
- Protein
- p.Ser3340=
- Coding
- c.10020G>A
- MANE Select
- NM_005045
- dbSNP
- rs760919496
- Type
- single nucleotide variant
- Location
- chr7:103483814 (GRCh38)
- Gene constraint
- LOEUF 0.276 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Similar variants
- RELN c.3912+2T>G Likely pathogenic ★★ same condition
- RELN c.7349+2T>C Likely pathogenic ★★ same condition
- RELN p.Arg1622Ter Pathogenic/Likely pathogenic ★★ same condition
- RELN c.1893-3C>T Uncertain significance ★★ same condition
- RELN c.227-3C>T Uncertain significance ★★ same condition
- RELN c.2465+5G>T Uncertain significance ★★ same condition
- RELN c.6072+3A>G Uncertain significance ★★ same condition
- RELN c.6072+4C>G 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/reln-p-ser3340 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown