Is LDLR p.Phe403= (c.1209C>T) pathogenic?

LDLR p.Phe403= (c.1209C>T) is classified Likely benign in LDLR (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-12-12). Ultra-rare (popmax 0.0176%, sas); Associated with familial hypercholesterolemia.

What condition is associated with LDLR p.Phe403= (c.1209C>T)?

LDLR p.Phe403= (c.1209C>T) is associated with familial hypercholesterolemia, hypercholesterolemia, familial, 1 (ClinVar).

How common is LDLR p.Phe403= (c.1209C>T) in the general population?

LDLR p.Phe403= (c.1209C>T) is ultra-rare (popmax 0.0176%, sas) (gnomAD).

LDLR p.Phe403=

c.1209C>T · rs777903106 · VCV1557053

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0176%, sas)

Conditions

familial hypercholesterolemia

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 0.79	GERP 0.43, phastCons 1
Overall
CADD	8.662	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0176% South Asian · 16/91,056 alleles

Filtering AF 0.011% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00889%

Overall 0.00105% 17/1,613,302 alleles · ultra-rare exomes 16/1,461,184 · genomes 1/152,118 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0176%	5,691
Remaining individualsnot grpmax-eligible	0.0016%	62,438

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.Phe403=
Coding: c.1209C>T
MANE Select: NM_000527
dbSNP: rs777903106
Type: single nucleotide variant
Location: chr19:11113300 (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

familial hypercholesterolemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hypercholesterolemia, familial, 1

Similar variants

LDLR p.Phe403Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
LDLR p.Phe403del Likely pathogenic ★★★ same residue
LDLR p.Phe403fs Pathogenic ★ same residue
LDLR p.Phe403Ser Likely pathogenic ★ same residue
LDLR c.1186+5G>A Likely pathogenic ★★★ same condition
LDLR c.1359-1G>A Pathogenic ★★★ same condition
LDLR c.1359-5C>G Likely pathogenic ★★★ same condition
LDLR c.1705+2T>C 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-phe403 (accessed [today's date]).

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