Is PCSK9 p.Val4= (c.12C>T) pathogenic?

PCSK9 p.Val4= (c.12C>T) is classified Likely benign in PCSK9 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-30). Very rare (popmax 6.39e-05%); Associated with hypercholesterolemia, autosomal dominant, 3.

What condition is associated with PCSK9 p.Val4= (c.12C>T)?

PCSK9 p.Val4= (c.12C>T) is associated with hypercholesterolemia, autosomal dominant, 3 (ClinVar).

How common is PCSK9 p.Val4= (c.12C>T) in the general population?

PCSK9 p.Val4= (c.12C>T) is very rare (popmax 6.39e-05%) (gnomAD).

PCSK9 p.Val4=

c.12C>T · rs2523162767 · VCV2870398

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 6.39e-05%)

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 -0.26	GERP -1.3
Overall
CADD	6.096	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.39e-05%

Overall 6.39e-05% 1/1,565,480 alleles · very rare exomes 1/1,413,110 · genomes 0/152,370 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PCSK9
Protein: p.Val4=
Coding: c.12C>T
MANE Select: NM_174936
dbSNP: rs2523162767
Type: single nucleotide variant
Location: chr1:55039849 (GRCh38)
Gene constraint: LOEUF 1.25 · pLI <0.01 · ClinGen HI dosage-sensitivity unlikely (gnomAD)
Structure: AlphaFold pLDDT 85.03 · 66 PDB

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.Val4Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
PCSK9 p.Val4Leu Uncertain significance ★ ⚠ 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

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-val4 (accessed [today's date]).

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