Is LRP2 p.Asp4530fs (c.13587dup) pathogenic?

LRP2 p.Asp4530fs (c.13587dup) is classified Pathogenic in LRP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-20). No gnomAD frequency available for this variant.

How common is LRP2 p.Asp4530fs (c.13587dup) in the general population?

LRP2 p.Asp4530fs (c.13587dup) is no gnomAD frequency available for this variant (gnomAD).

LRP2 p.Asp4530fs

c.13587dup · rs2545639161 · VCV2839301

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

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 LoF-intolerant gene
NMD	predicted	premature termination codon in exon 76 of 79
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 2.4, phastCons 1

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: LRP2
Protein: p.Asp4530fs
Coding: c.13587dup
MANE Select: NM_004525
dbSNP: rs2545639161
Type: Duplication
Location: chr2:169137424 (GRCh38)
Gene constraint: LOEUF 0.352 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)

Full LRP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

LRP2 p.Cys4381fs Pathogenic/Likely pathogenic ★★ same type
LRP2 c.11014+2dup Uncertain significance ★★ same type
LRP2 c.1975+2_1975+5dup Uncertain significance ★★ same type
LRP2 c.7384_7390+8dup Uncertain significance ★★ same type
LRP2 c.4295-10dup Benign/Likely benign ★★ same type
LRP2 c.770-4dup Likely benign ★★ same type
LRP2 c.7716-13dup Benign/Likely benign ★★ same type
LRP2 p.Ala1265fs Pathogenic ★ same type

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/lrp2-p-asp4530fs (accessed [today's date]).

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