Is LDLR p.Asp133Ala (c.398A>C) pathogenic?

LDLR p.Asp133Ala (c.398A>C) is classified Conflicting classifications of pathogenicity in LDLR (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2025-07-11). AlphaMissense: likely pathogenic (0.9953); Very rare (popmax 0.00133%, afr); Associated with familial hypercholesterolemia.

What condition is associated with LDLR p.Asp133Ala (c.398A>C)?

LDLR p.Asp133Ala (c.398A>C) is associated with familial hypercholesterolemia, hypercholesterolemia, familial, 1 (ClinVar).

How common is LDLR p.Asp133Ala (c.398A>C) in the general population?

LDLR p.Asp133Ala (c.398A>C) is very rare (popmax 0.00133%, afr) (gnomAD).

What do computational predictors say about LDLR p.Asp133Ala (c.398A>C)?

AlphaMissense predicts likely pathogenic (score 0.9953) — an in-silico prediction, not a clinical call.

LDLR p.Asp133Ala

c.398A>C · rs1317204420 · VCV577814

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

AlphaMissense

likely pathogenic

0.9953 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

familial hypercholesterolemia

Computational evidence

Protein change
AlphaMissense	0.9953	likely pathogenic · top 3% in LDLR
REVEL	0.95	strongly pathogenic-leaning
SaProt	LLR -13.39	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.5, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 42 kb · p 0.91 · regional, not allelic
Overall
CADD	25.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/74,920 alleles

Overall 0.000657% 1/152,116 alleles · very rare

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: LDLR
Protein: p.Asp133Ala
Coding: c.398A>C
MANE Select: NM_000527
dbSNP: rs1317204420
Type: single nucleotide variant
Location: chr19:11105304 (GRCh38)
Gene constraint: LOEUF 1.091 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.81 · 36 PDB
Residue 133: a disulfide bond; the ldl-receptor class a 3 domain

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

Also linked: hypercholesterolemia, familial, 1

Similar variants

LDLR p.Asp133= Likely benign ★★ same residue
LDLR p.Asp133Gly Likely pathogenic ★ same residue
LDLR p.Asp133His Pathogenic ★ same residue
LDLR p.Asp133Tyr Likely pathogenic ★ same residue
LDLR p.Asp133Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
LDLR p.Asp133fs Pathogenic ★ same residue
LDLR c.1186+5G>A Likely pathogenic ★★★ same condition
LDLR c.1359-1G>A 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-asp133ala (accessed [today's date]).

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