Is SCN2B p.Val34= (c.102A>G) pathogenic?

SCN2B p.Val34= (c.102A>G) is classified Likely benign in SCN2B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-29). Absent from gnomAD v4.1.

How common is SCN2B p.Val34= (c.102A>G) in the general population?

SCN2B p.Val34= (c.102A>G) is absent from gnomAD v4.1 (gnomAD).

SCN2B p.Val34=

c.102A>G · VCV3629487

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -0.61	GERP -3, phastCons 0.017
Overall
CADD	5.506	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SCN2B
Protein: p.Val34=
Coding: c.102A>G
MANE Select: NM_004588
Type: single nucleotide variant
Location: chr11:118168720 (GRCh38)
Gene constraint: LOEUF 1.15 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.03 · 35 PDB
Residue 34: the ig-like c2-type domain

Full SCN2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SCN2B p.Val34Glu Uncertain significance ★ ⚠ same residue
SCN2B p.Ala171Pro Uncertain significance ★★ ⚠ same type
SCN2B p.Arg135Cys Uncertain significance ★★ ⚠ same type
SCN2B p.Arg135His Uncertain significance ★★ same type
SCN2B p.Arg137His Uncertain significance ★★ ⚠ same type
SCN2B p.Arg154Gln Uncertain significance ★★ ⚠ same type
SCN2B p.Arg185Thr Uncertain significance ★★ ⚠ same type
SCN2B p.Arg84Cys 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/scn2b-p-val34 (accessed [today's date]).

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