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UniProtKB/Swiss-Prot P01130: Variant p.Arg416Trp

Low-density lipoprotein receptor
Gene: LDLR
Variant information

Variant position:  416
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  LP/P [Disclaimer]
The variants are classified into three categories: LP/P, LB/B and US.
  • LP/P: likely pathogenic or pathogenic.
  • LB/B: likely benign or benign.
  • US: uncertain significance

Residue change:  From Arginine (R) to Tryptophan (W) at position 416 (R416W, p.Arg416Trp).
Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.

Physico-chemical properties:  Change from large size and basic (R) to large size and aromatic (W)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -3
The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:
  • Lowest score: -4 (low probability of substitution).
  • Highest score: 11 (high probability of substitution).
More information can be found on the following page

Variant description:  In FHCL1; results in reduced receptor expression at the cell surface due to defective receptor recycling.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  416
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  860
The length of the canonical sequence.

Location on the sequence:   GSIAYLFFTNRHEVRKMTLD  R SEYTSLIPNLRNVVALDTEV
The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.

Residue conservation: 
The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         GSIAYLFFTNRHEVRKMTLDRSEYTSLIPNLRNVVALDTEV

Mouse                         GSIGYLLFTNRHEVRKMTLDRSEYTSLLPNLKNVVALDTEV

Rat                           GSIGFLLFTNRHEVRKMTLDRSEYTSLIPNLKNVVALDTEV

Bovine                        GTIAYLFFTNRHEVRKMTLDRSEYTSLIPNLKNVVALDTEV

Sequence annotation in neighborhood:  
The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:
  • Type: the type of sequence feature.
  • Positions: endpoints of the sequence feature.
  • Description: contains additional information about the feature.

TypePositionsDescription
Chain 22 – 860 Low-density lipoprotein receptor
Topological domain 22 – 788 Extracellular
Repeat 397 – 438 LDL-receptor class B 1


Literature citations

Spectrum of LDL receptor gene mutations in heterozygous familial hypercholesterolemia.
Day I.N.M.; Whittall R.A.; O'Dell S.D.; Haddad L.; Bolla M.K.; Gudnason V.; Humphries S.E.;
Hum. Mutat. 10:116-127(1997)
Cited for: VARIANTS FHCL1 TRP-27; CYS-78; GLY-87; TYR-89; ASN-90; GLY-90; LYS-101; TYR-160; ASN-168; LEU-177; GLY-221; GLU-227; ARG-286; TYR-313; TYR-327; ASN-342; PRO-350; ASP-399; TRP-416; HIS-482; ARG-483; SER-526; ASP-549; CYS-633; LEU-649 AND ILE-726;

Molecular genetics of familial hypercholesterolaemia in Norway.
Leren T.P.; Tonstad S.; Gundersen K.E.; Bakken K.S.; Rodningen O.K.; Sundvold H.; Ose L.; Berg K.;
J. Intern. Med. 241:185-194(1997)
Cited for: VARIANTS FHCL1 PRO-56; TYR-175; TYR-356; VAL-401 AND TRP-416;

Genetic diagnosis of familial hypercholesterolemia using a DNA-array based platform.
Alonso R.; Defesche J.C.; Tejedor D.; Castillo S.; Stef M.; Mata N.; Gomez-Enterria P.; Martinez-Faedo C.; Forga L.; Mata P.;
Clin. Biochem. 42:899-903(2009)
Cited for: VARIANTS FHCL1 TYR-155; GLY-300; GLY-301; TRP-416 AND ASN-454;

Functional characterization and classification of frequent low-density lipoprotein receptor variants.
Etxebarria A.; Benito-Vicente A.; Palacios L.; Stef M.; Cenarro A.; Civeira F.; Ostolaza H.; Martin C.;
Hum. Mutat. 36:129-141(2015)
Cited for: CHARACTERIZATION OF VARIANTS FHCL1 TYR-155; TRP-416; ASN-454; GLY-577 AND LYS-825;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.