Is LDLR p.Phe403Ser (c.1208T>C) pathogenic?

LDLR p.Phe403Ser (c.1208T>C) is classified Likely pathogenic in LDLR (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-02). AlphaMissense: likely pathogenic (0.9821); Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with LDLR p.Phe403Ser (c.1208T>C)?

LDLR p.Phe403Ser (c.1208T>C) is associated with Cardiovascular phenotype (ClinVar).

How common is LDLR p.Phe403Ser (c.1208T>C) in the general population?

LDLR p.Phe403Ser (c.1208T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about LDLR p.Phe403Ser (c.1208T>C)?

AlphaMissense predicts likely pathogenic (score 0.9821) — an in-silico prediction, not a clinical call.

LDLR p.Phe403Ser

c.1208T>C · rs2516003230 · VCV2568145

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9821 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.9821	likely pathogenic ✓ concordant with ClinVar · top 9% in LDLR
REVEL	0.936	strongly pathogenic-leaning
SaProt	LLR -16.43	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 7.8	GERP 2.5, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 42 kb · p 0.91 · regional, not allelic
Overall
CADD	28.3	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: LDLR
Protein: p.Phe403Ser
Coding: c.1208T>C
MANE Select: NM_000527
dbSNP: rs2516003230
Type: single nucleotide variant
Location: chr19:11113299 (GRCh38)
Gene constraint: LOEUF 1.091 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.81 · 36 PDB
Residue 403: a UniProt-annotated variant site (in fhcl1); a β-strand

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LDLR p.Phe403Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
LDLR p.Phe403= Likely benign ★★ same residue
LDLR p.Phe403del Likely pathogenic ★★★ same residue
LDLR c.1061-1G>C Pathogenic/Likely pathogenic ★★ same condition
LDLR c.1186+1G>T Pathogenic ★★ same condition
LDLR c.1186+2T>G Pathogenic/Likely pathogenic ★★ same condition
LDLR c.1586+1G>A Pathogenic/Likely pathogenic ★★ same condition
LDLR c.1587-1G>A 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-phe403ser (accessed [today's date]).

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