Is PCSK9 p.Val79= (c.237G>A) pathogenic?

PCSK9 p.Val79= (c.237G>A) is classified Likely benign in PCSK9 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-07). Absent from gnomAD v4.1; Associated with hypercholesterolemia, autosomal dominant, 3.

What condition is associated with PCSK9 p.Val79= (c.237G>A)?

PCSK9 p.Val79= (c.237G>A) is associated with hypercholesterolemia, autosomal dominant, 3 (ClinVar).

How common is PCSK9 p.Val79= (c.237G>A) in the general population?

PCSK9 p.Val79= (c.237G>A) is absent from gnomAD v4.1 (gnomAD).

PCSK9 p.Val79=

c.237G>A · rs2523182849 · VCV1932303

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hypercholesterolemia, autosomal dominant, 3

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 0.3	GERP 0.017, phastCons 0.99
Overall
CADD	7.499	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: PCSK9
Protein: p.Val79=
Coding: c.237G>A
MANE Select: NM_174936
dbSNP: rs2523182849
Type: single nucleotide variant
Location: chr1:55043872 (GRCh38)
Gene constraint: LOEUF 1.25 · pLI <0.01 · ClinGen HI dosage-sensitivity unlikely (gnomAD)
Structure: AlphaFold pLDDT 85.03 · 66 PDB
Residue 79: the inhibitor i9 domain; a β-strand

Full PCSK9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hypercholesterolemia, autosomal dominant, 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PCSK9 p.Val79Met Conflicting classifications of pathogenicity ★ ⚠ same residue
PCSK9 p.Arg215His Pathogenic/Likely pathogenic ★★ ⚠ same condition
PCSK9 p.Asp374His Pathogenic/Likely pathogenic ★★ ⚠ same condition
PCSK9 p.Asp374Tyr Pathogenic/Likely pathogenic ★★ ⚠ same condition
PCSK9 c.1863+1G>A Uncertain significance ★★ same condition
PCSK9 c.1864-12G>A Uncertain significance ★★ same condition
PCSK9 c.207+5G>A Uncertain significance ★★ same condition
PCSK9 c.207+6G>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/pcsk9-p-val79 (accessed [today's date]).

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