Is LDLR p.Cys803Arg (c.2407T>C) pathogenic?

LDLR p.Cys803Arg (c.2407T>C) is classified Likely pathogenic in LDLR (ClinVar, Single submitter, 1 submitter; last evaluated 2016-11-05). AlphaMissense: likely pathogenic (0.95); Absent from gnomAD v4.1; Associated with hypercholesterolemia, familial, 1.

What condition is associated with LDLR p.Cys803Arg (c.2407T>C)?

LDLR p.Cys803Arg (c.2407T>C) is associated with hypercholesterolemia, familial, 1 (ClinVar).

How common is LDLR p.Cys803Arg (c.2407T>C) in the general population?

LDLR p.Cys803Arg (c.2407T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about LDLR p.Cys803Arg (c.2407T>C)?

AlphaMissense predicts likely pathogenic (score 0.95) — an in-silico prediction, not a clinical call.

LDLR p.Cys803Arg

c.2407T>C · rs1060499930 · VCV403648

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.95 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

hypercholesterolemia, familial, 1

Computational evidence

Protein change
AlphaMissense	0.95	likely pathogenic ✓ concordant with ClinVar
REVEL	0.441	indeterminate
SaProt	LLR -11.76	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>A here scores Δ0.61 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.42	GERP -3.1, phastCons 0.054
Regional constraint	o/e 1.00	unconstrained · MANE · 42 kb · p 0.91 · regional, not allelic
Overall
CADD	13.69	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: LDLR
Protein: p.Cys803Arg
Coding: c.2407T>C
MANE Select: NM_000527
dbSNP: rs1060499930
Type: single nucleotide variant
Location: chr19:11129530 (GRCh38)
Gene constraint: LOEUF 1.091 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.81 · 36 PDB

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

Disease context

hypercholesterolemia, familial, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LDLR p.Cys803= Likely benign ★★ same residue
LDLR p.Cys803_Leu808dup Uncertain significance ★★★ same residue
LDLR p.Cys803_Leu808del Conflicting classifications of pathogenicity ★ same residue
LDLR p.Cys803Ser Uncertain significance ★ ⚠ 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.1705+2T>C Likely 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-cys803arg (accessed [today's date]).

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