Is LDLR p.Arg850= (c.2550A>G) pathogenic?

LDLR p.Arg850= (c.2550A>G) is classified Likely benign in LDLR (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-03). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with LDLR p.Arg850= (c.2550A>G)?

LDLR p.Arg850= (c.2550A>G) is associated with Cardiovascular phenotype (ClinVar).

How common is LDLR p.Arg850= (c.2550A>G) in the general population?

LDLR p.Arg850= (c.2550A>G) is absent from gnomAD v4.1 (gnomAD).

LDLR p.Arg850=

c.2550A>G · VCV4046740

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

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 Δ0.27 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.95	GERP -1.7, phastCons 0.99
Overall
CADD	10.11	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: LDLR
Protein: p.Arg850=
Coding: c.2550A>G
MANE Select: NM_000527
Type: single nucleotide variant
Location: chr19:11131283 (GRCh38)
Gene constraint: LOEUF 1.091 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.81 · 36 PDB
Residue 850: the 'required for mylip-triggered down-regulation of ldlr' region

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LDLR p.Arg850Lys Uncertain significance ★ ⚠ same residue
LDLR c.1061-1G>C Pathogenic/Likely pathogenic ★★ same condition
LDLR c.1186+1G>T Pathogenic ★★ same condition
LDLR c.1186+2T>G Pathogenic/Likely pathogenic ★★ same condition
LDLR c.1586+1G>A Pathogenic/Likely pathogenic ★★ same condition
LDLR c.1587-1G>A Pathogenic/Likely pathogenic ★★ same condition
LDLR c.1587-2A>G Pathogenic/Likely pathogenic ★★ same condition
LDLR c.1587-2A>T Pathogenic/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-arg850 (accessed [today's date]).

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