Is SLC52A2 p.Val331= (c.993G>A) pathogenic?

SLC52A2 p.Val331= (c.993G>A) is classified Likely benign in SLC52A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-14). No allele count reported in gnomAD v4.1 (AN 1,599,118); Associated with Brown-Vialetto-van Laere syndrome 2.

What condition is associated with SLC52A2 p.Val331= (c.993G>A)?

SLC52A2 p.Val331= (c.993G>A) is associated with Brown-Vialetto-van Laere syndrome 2 (ClinVar).

How common is SLC52A2 p.Val331= (c.993G>A) in the general population?

SLC52A2 p.Val331= (c.993G>A) is no allele count reported in gnomAD v4.1 (AN 1,599,118) (gnomAD).

SLC52A2 p.Val331=

c.993G>A · VCV4707277

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,599,118)

Conditions

Brown-Vialetto-van Laere syndrome 2

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 0.58	GERP -3.4, phastCons 1
Overall
CADD	3.333	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,599,118). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SLC52A2
Protein: p.Val331=
Coding: c.993G>A
MANE Select: NM_001363118
Type: single nucleotide variant
Location: chr8:144360485 (GRCh38)
Gene constraint: LOEUF 0.955 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.50 · 1 PDB

Full SLC52A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Brown-Vialetto-van Laere syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SLC52A2 c.131-1G>C Likely pathogenic ★★ same condition
SLC52A2 p.Ala420Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
SLC52A2 p.Cys325Gly Likely pathogenic ★★ ⚠ same condition
SLC52A2 p.Gln270Ter Pathogenic/Likely pathogenic ★★ same condition
SLC52A2 p.Gly306Arg Pathogenic ★★ same condition
SLC52A2 p.Gly306Glu Likely pathogenic ★★ same condition
SLC52A2 p.Leu312Pro Pathogenic/Likely pathogenic ★★ same condition
SLC52A2 p.Leu339Pro Pathogenic ★★ 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/slc52a2-p-val331 (accessed [today's date]).

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