Is LDLR p.Asp266fs (c.796_799del) pathogenic?

LDLR p.Asp266fs (c.796799del) is classified Pathogenic in LDLR (ClinVar, Single submitter, 1 submitter; last evaluated 2016-03-25). No gnomAD frequency available for this variant; Associated with hypercholesterolemia, familial, 1.

What condition is associated with LDLR p.Asp266fs (c.796_799del)?

LDLR p.Asp266fs (c.796_799del) is associated with hypercholesterolemia, familial, 1 (ClinVar).

How common is LDLR p.Asp266fs (c.796_799del) in the general population?

LDLR p.Asp266fs (c.796_799del) is no gnomAD frequency available for this variant (gnomAD).

LDLR p.Asp266fs

c.796_799del · rs879254677 · VCV251455

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hypercholesterolemia, familial, 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 5 of 18
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -10	GERP -3.7

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: LDLR
Protein: p.Asp266fs
Coding: c.796_799del
MANE Select: NM_000527
dbSNP: rs879254677
Type: Deletion
Location: chr19:11106666 (GRCh38)
Gene constraint: LOEUF 1.091 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.81 · 36 PDB
Residue 266: the ldl-receptor class a 6 domain; a UniProt-annotated variant site (in fhcl1; pathogenic; cincinnati-1); an α-helix

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.Asp266Asn Pathogenic ★★★ same residue
LDLR p.Asp266Glu Pathogenic ★★★ same residue
LDLR p.Asp266Gly Likely pathogenic ★★★ same residue
LDLR p.Asp266Tyr Pathogenic ★★★ same residue
LDLR p.Asp266Val Likely pathogenic ★★★ same residue
LDLR p.Asp266His Pathogenic/Likely pathogenic ★★ same residue
LDLR p.Ala612fs Likely pathogenic ★★★ same condition
LDLR p.Lys816fs 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-asp266fs (accessed [today's date]).

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