Is RELN p.Ala3358= (c.10074A>G) pathogenic?

RELN p.Ala3358= (c.10074A>G) is classified Benign in RELN (ClinVar, Multiple submitters, 13 submitters; last evaluated 2026-02-03). Common (popmax 34.9%, afr) — too common for a highly-penetrant pathogenic allele; Associated with Norman-Roberts syndrome.

What condition is associated with RELN p.Ala3358= (c.10074A>G)?

RELN p.Ala3358= (c.10074A>G) is associated with Norman-Roberts syndrome, familial temporal lobe epilepsy 7 (ClinVar).

RELN p.Ala3358=

Q: How common is RELN p.Ala3358= (c.10074A>G) in the general population?

RELN p.Ala3358= (c.10074A>G) is common (popmax 34.9%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.10074A>G · rs1062831 · VCV95209

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 13 submitters

gnomAD v4.1

Common

common (popmax 34.9%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

Norman-Roberts syndrome

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 -20	GERP -3.9
Overall
CADD	0.007	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 34.9% African / African-American · 26,151/74,982 alleles

Filtering AF 34.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 34.4%

Overall 11.1% 178,541/1,613,946 alleles · common exomes 152,127/1,461,700 · genomes 26,414/152,246 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	34.9%	3
East Asian	26%	4
South Asian	17.2%	6
Remaining individualsnot grpmax-eligible	12.3%	8
Admixed American	12.2%	8
Middle Eastern	12%	8
Amishnot grpmax-eligible	11.4%	9
European (non-Finnish)	8.74%	11
Ashkenazi Jewishnot grpmax-eligible	8.54%	12
Finnishnot grpmax-eligible	5.57%	18

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.Ala3358=
Coding: c.10074A>G
MANE Select: NM_005045
dbSNP: rs1062831
Type: single nucleotide variant
Location: chr7:103483760 (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

Norman-Roberts syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: familial temporal lobe epilepsy 7

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-ala3358 (accessed [today's date]).

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