Is OSBPL2 p.Pro180= (c.540C>G) pathogenic?

OSBPL2 p.Pro180= (c.540C>G) is classified Likely benign in OSBPL2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-17). Absent from gnomAD v4.1.

How common is OSBPL2 p.Pro180= (c.540C>G) in the general population?

OSBPL2 p.Pro180= (c.540C>G) is absent from gnomAD v4.1 (gnomAD).

OSBPL2 p.Pro180=

c.540C>G · rs1568846625 · VCV1665703

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 -4	GERP -5.3
Overall
CADD	0.269	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: OSBPL2
Protein: p.Pro180=
Coding: c.540C>G
MANE Select: NM_144498
dbSNP: rs1568846625
Type: single nucleotide variant
Location: chr20:62279205 (GRCh38)
Gene constraint: LOEUF 0.467 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 83.92 · 1 PDB

Full OSBPL2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

OSBPL2 p.Ala442Val Uncertain significance ★★ ⚠ same type
OSBPL2 p.Arg434Trp Uncertain significance ★★ same type
OSBPL2 p.Asp475Asn Uncertain significance ★★ ⚠ same type
OSBPL2 p.Gln125Pro Uncertain significance ★★ ⚠ same type
OSBPL2 p.Gln58Pro Uncertain significance ★★ ⚠ same type
OSBPL2 p.Glu284Gly Uncertain significance ★★ same type
OSBPL2 p.Gly149Ser Uncertain significance ★★ ⚠ same type
OSBPL2 p.Gly245Arg 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/osbpl2-p-pro180 (accessed [today's date]).

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