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Table 3 The predicted pathogenic variants

From: Analysis of sequence variations in low-density lipoprotein receptor gene among Malaysian patients with familial hypercholesterolemia

Name of Variant

Location

Analysis by NNSPLICE

Analysis by AST

Alamut

Uni prot report

Poly Phen

c.190+4A>T

Intron 2

Before mutation the score was 0.54. After mutation,not recognized as splice site

Before change the score was 70.3 and ΔG -3.6

After mutation the score was 60.32 and ΔG -3.0

   

c.301G>A;p.Glu101Lys

Exon 3

  

Possibly pathogenic

as reported by UniProt (FTId: VAR_005315)

Change from medium size and acidic (E) to large size and basic (K)

 

c.415G>C;p.Asp139His

Exon 4

    

Changes in amino acid.

Disruption of ligand binding site

c.601G>A;p.Glu201Lys

Exon 4

    

Changes in amino acid.

Disruption of ligand binding site

c.763T>A;p.Cys255Ser

Exon 5

    

Changes in amino acid.

Disruption of ligand binding site

c.1706_1845dup;p.Asp616IlefsX96

Exon 12

  

Pathogenic

This duplication creates a frame shift starting at codon Asp616. The new reading frame ends in a STOP codon 95 positions downstream.

The mRNA produced might be targeted for nonsense mediated decay (NMD).

 

c.1996_2012del;p.Trp666ProfsX45

Exon 14

  

Pathogenic

This deletion creates a frame shift starting at codon Trp666. The new reading frame ends in a STOP codon 44 positions downstream.

The mRNA produced might be targeted for nonsense mediated decay (NMD).

 

c.2100C>G;p.Asp700Glu

Exon 14

  

Possibly pathogenic

as reported by UniProt (FTId: VAR_005412)

Change in 3 D structure of protein

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