LDLR p.Asn439fs
c.1316del · VCV4940699
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
LDLR-related disorder
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 haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 9 of 18 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -1.8, phastCons 0.99 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- LDLR
- Protein
- p.Asn439fs
- Coding
- c.1316del
- MANE Select
- NM_000527
- Type
- Deletion
- Location
- chr19:11113406 (GRCh38)
- Gene constraint
- LOEUF 1.091 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.81 · 36 PDB
- Residue 439
- a turn
Disease context
LDLR-related disorder
Similar variants
- LDLR c.940_940+14del Pathogenic ★★ same condition
- LDLR p.Asn439Tyr Likely pathogenic ★★ ⚠ same residue
- LDLR p.Pro309fs Pathogenic ★★ same condition
- LDLR p.Asn439Lys Uncertain significance ★★ ⚠ same residue
- LDLR p.Asn439Ser Uncertain significance ★★ ⚠ same residue
- LDLR p.Asp320fs Likely pathogenic ★ same condition
- LDLR p.Gln660fs Likely pathogenic ★ same condition
- LDLR p.His769fs 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-asn439fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown