Is LDLR p.Ser586= (c.1758A>G) pathogenic?

LDLR p.Ser586= (c.1758A>G) is classified Likely benign in LDLR (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-11-14). Very rare (popmax 0.000933%, nfe); Associated with familial hypercholesterolemia.

What condition is associated with LDLR p.Ser586= (c.1758A>G)?

LDLR p.Ser586= (c.1758A>G) is associated with familial hypercholesterolemia (ClinVar).

How common is LDLR p.Ser586= (c.1758A>G) in the general population?

LDLR p.Ser586= (c.1758A>G) is very rare (popmax 0.000933%, nfe) (gnomAD).

LDLR p.Ser586=

c.1758A>G · rs2512416394 · VCV1949963

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.000933%, nfe)

Conditions

familial hypercholesterolemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>T here scores Δ0.60 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.23	GERP -2, phastCons 0.21
Overall
CADD	3.502	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000933% European (non-Finnish) · 11/1,179,338 alleles

Filtering AF 0.000501% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000366%

Overall 0.000682% 11/1,613,170 alleles · very rare exomes 11/1,461,088 · genomes 0/152,082 · 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: LDLR
Protein: p.Ser586=
Coding: c.1758A>G
MANE Select: NM_000527
dbSNP: rs2512416394
Type: single nucleotide variant
Location: chr19:11116911 (GRCh38)
Gene constraint: LOEUF 1.091 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.81 · 36 PDB
Residue 586: a β-strand

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

Disease context

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

Similar variants

LDLR p.Ser586Pro Likely pathogenic ★ same residue
LDLR p.Ser586Ter Pathogenic ★ same residue
LDLR c.1186+5G>A Likely pathogenic ★★★ same condition
LDLR c.1359-1G>A Pathogenic ★★★ same condition
LDLR c.1359-5C>G Likely pathogenic ★★★ same condition
LDLR c.190+4A>T Likely pathogenic ★★★ same condition
LDLR c.2140+1G>A Pathogenic ★★★ same condition
LDLR c.2389+2T>G 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/ldlr-p-ser586 (accessed [today's date]).

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