Is RELN p.Ser3170= (c.9510C>T) pathogenic?

RELN p.Ser3170= (c.9510C>T) is classified Likely benign in RELN (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-21). Very rare (popmax 0.00267%, afr); Associated with familial temporal lobe epilepsy 7.

What condition is associated with RELN p.Ser3170= (c.9510C>T)?

RELN p.Ser3170= (c.9510C>T) is associated with familial temporal lobe epilepsy 7, Norman-Roberts syndrome (ClinVar).

How common is RELN p.Ser3170= (c.9510C>T) in the general population?

RELN p.Ser3170= (c.9510C>T) is very rare (popmax 0.00267%, afr) (gnomAD).

RELN p.Ser3170=

c.9510C>T · rs1562847406 · VCV2418316

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Conditions

familial temporal lobe epilepsy 7

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.59	GERP -0.94, phastCons 0.99
Overall
CADD	14.43	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/75,042 alleles

Filtering AF 0.000442% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000166%

Overall 0.000248% 4/1,614,184 alleles · very rare exomes 4/1,461,878 · genomes 0/152,306 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,521
Remaining individualsnot grpmax-eligible	0.0016%	62,510
European (non-Finnish)	8.47e-05%	1,180,036

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.Ser3170=
Coding: c.9510C>T
MANE Select: NM_005045
dbSNP: rs1562847406
Type: single nucleotide variant
Location: chr7:103490763 (GRCh38)

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

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-ser3170 (accessed [today's date]).

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