Is RELN p.Ala302= (c.906C>T) pathogenic?

RELN p.Ala302= (c.906C>T) is classified Benign/Likely benign in RELN (ClinVar, Multiple submitters, 10 submitters; last evaluated 2026-03-01). Rare (popmax 0.916%, afr); Associated with familial temporal lobe epilepsy 7.

What condition is associated with RELN p.Ala302= (c.906C>T)?

RELN p.Ala302= (c.906C>T) is associated with familial temporal lobe epilepsy 7, Norman-Roberts syndrome (ClinVar).

How common is RELN p.Ala302= (c.906C>T) in the general population?

RELN p.Ala302= (c.906C>T) is rare (popmax 0.916%, afr) (gnomAD).

RELN p.Ala302=

c.906C>T · rs114494558 · VCV193677

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

gnomAD v4.1

Rare

rare (popmax 0.916%, afr)

Conditions

familial temporal lobe epilepsy 7

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.8	GERP 0.15, phastCons 1
Overall
CADD	7.6	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.916% African / African-American · 687/74,998 alleles

Filtering AF 0.859% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.837%

Overall 0.0467% 754/1,613,654 alleles · rare exomes 357/1,461,412 · genomes 397/152,242 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.916%	109
Remaining individualsnot grpmax-eligible	0.0512%	1,952
Middle Eastern	0.0495%	2,019
Admixed American	0.0484%	2,068
Finnishnot grpmax-eligible	0.00156%	64,016
European (non-Finnish)	0.00017%	589,856

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.Ala302=
Coding: c.906C>T
MANE Select: NM_005045
dbSNP: rs114494558
Type: single nucleotide variant
Location: chr7:103698090 (GRCh38)
Gene constraint: LOEUF 0.276 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)

Full RELN gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

familial temporal lobe epilepsy 7 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Norman-Roberts syndrome

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-ala302 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown