Is LDLR p.Asp301fs (c.901_911del) pathogenic?

LDLR p.Asp301fs (c.901911del) is classified Pathogenic in LDLR (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-23). No gnomAD frequency available for this variant; Associated with familial hypercholesterolemia.

What condition is associated with LDLR p.Asp301fs (c.901_911del)?

LDLR p.Asp301fs (c.901_911del) is associated with familial hypercholesterolemia (ClinVar).

How common is LDLR p.Asp301fs (c.901_911del) in the general population?

LDLR p.Asp301fs (c.901_911del) is no gnomAD frequency available for this variant (gnomAD).

LDLR p.Asp301fs

c.901_911del · rs2077313770 · VCV962562

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

familial hypercholesterolemia

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 6 of 18
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.079	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.Asp301fs
Coding: c.901_911del
MANE Select: NM_000527
dbSNP: rs2077313770
Type: Deletion
Location: chr19:11107473 (GRCh38)
Gene constraint: LOEUF 1.091 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.81 · 36 PDB
Residue 301: the ldl-receptor class a 7 domain; a UniProt-annotated variant site (in fhcl1); a UniProt-annotated variant site (in fhcl1; does not affect receptor expression at the cell surface; results in reduced ldl binding; results in reduced ldl uptake and internalization)

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.Asp301Gly Pathogenic/Likely pathogenic ★★ same residue
LDLR p.Asp301Tyr Pathogenic/Likely pathogenic ★★ same residue
LDLR p.Asp301Val Pathogenic ★ same residue
LDLR p.Asp301= Likely benign ★ same residue
LDLR p.Lys816fs Likely pathogenic ★★★ same condition
LDLR p.Tyr400_Phe402del Likely pathogenic ★★★ same condition
LDLR p.Phe86_Arg88del Uncertain significance ★★★ same condition
LDLR c.1056_1060+3del 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-asp301fs (accessed [today's date]).

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