Is SCARB2 p.Pro439= (c.1317C>G) pathogenic?

SCARB2 p.Pro439= (c.1317C>G) is classified Likely benign in SCARB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-09-19). Absent from gnomAD v4.1; Associated with progressive myoclonus epilepsy.

What condition is associated with SCARB2 p.Pro439= (c.1317C>G)?

SCARB2 p.Pro439= (c.1317C>G) is associated with progressive myoclonus epilepsy (ClinVar).

How common is SCARB2 p.Pro439= (c.1317C>G) in the general population?

SCARB2 p.Pro439= (c.1317C>G) is absent from gnomAD v4.1 (gnomAD).

SCARB2 p.Pro439=

c.1317C>G · rs1731937017 · VCV1091191

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

progressive myoclonus epilepsy

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 0.95	GERP -3.8, phastCons 1
Overall
CADD	9.059	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: SCARB2
Protein: p.Pro439=
Coding: c.1317C>G
MANE Select: NM_005506
dbSNP: rs1731937017
Type: single nucleotide variant
Location: chr4:76163306 (GRCh38)
Gene constraint: LOEUF 0.683 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 93.01 · 10 PDB

Full SCARB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

progressive myoclonus epilepsy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SCARB2 p.Pro439Arg Uncertain significance ★ ⚠ same residue
SCARB2 p.Pro439Leu Uncertain significance ★ ⚠ same residue
SCARB2 c.704+1G>A Pathogenic ★★ same condition
SCARB2 p.Arg121Ter Pathogenic/Likely pathogenic ★★ same condition
SCARB2 p.Arg424Ter Pathogenic ★★ same condition
SCARB2 p.Gln288Ter Pathogenic ★★ same condition
SCARB2 p.Gln30Ter Pathogenic/Likely pathogenic ★★ same condition
SCARB2 c.1188-3T>C 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/scarb2-p-pro439 (accessed [today's date]).

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