Is LRP1 p.Asp1007= (c.3021C>T) pathogenic?

LRP1 p.Asp1007= (c.3021C>T) is classified Likely benign in LRP1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-07-09). Very rare (popmax 0.00893%, eas).

How common is LRP1 p.Asp1007= (c.3021C>T) in the general population?

LRP1 p.Asp1007= (c.3021C>T) is very rare (popmax 0.00893%, eas) (gnomAD).

LRP1 p.Asp1007=

c.3021C>T · rs762328607 · VCV2643115

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00893%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -20	GERP -5
Overall
CADD	4.313	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00893% East Asian · 4/44,784 alleles

Filtering AF 0.00298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0018%

Overall 0.00186% 30/1,611,574 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00893%	11,196
Remaining individualsnot grpmax-eligible	0.00802%	12,472
African / African-American	0.004%	24,969
Admixed American	0.00167%	59,964
European (non-Finnish)	0.00136%	73,628
South Asian	0.0011%	91,024

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: LRP1
Protein: p.Asp1007=
Coding: c.3021C>T
MANE Select: NM_173177 · reported on NM_002332
dbSNP: rs762328607
Type: single nucleotide variant
Location: chr12:57169165 (GRCh38)
Structure: AlphaFold pLDDT 88.37

Full LRP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

LRP1 p.Ala1564Thr Uncertain significance ★★ same type
LRP1 p.Arg228Gln Uncertain significance ★★ same type
LRP1 p.Arg2440Trp Uncertain significance ★★ ⚠ same type
LRP1 p.Arg539Gln Uncertain significance ★★ same type
LRP1 p.Asp4483Tyr Uncertain significance ★★ same type
LRP1 p.Ser2907Pro Uncertain significance ★★ same type
LRP1 p.Val3296Ile Uncertain significance ★★ ⚠ same type
C1D p.Glu4= Benign ★★ 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/lrp1-p-asp1007 (accessed [today's date]).

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