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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q14563: Variant p.Arg66Trp

Semaphorin-3A
Gene: SEMA3A
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Variant information Variant position: help 66 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help 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: help From Arginine (R) to Tryptophan (W) at position 66 (R66W, p.Arg66Trp). 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: help 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: help -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: help In HH16; phenotype consistent with Kallmann syndrome. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 66 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 771 The length of the canonical sequence.
Location on the sequence: help ITFNGLANSSSYHTFLLDEE R SRLYVGAKDHIFSFDLVNIK 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: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         ITFNGLANSSSYHTFLLDEERSRLYVGAKDHIFSFDLVNIK

Mouse                         ITFNGLANSSSYHTFLLDEERSRLYVGAKDHIFSFNLVNIK

Rat                           ITFNGLANSSSYHTFLLDEERSRLYVGAKDHIFSFNLVNIK

Chicken                       VNFNGLANSSSYHTFLLDEERSRLYVGAKDHIFSFNLVNIK
Sequence annotation in neighborhood: help 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 21 – 771 Semaphorin-3A
Domain 31 – 514 Sema
Glycosylation 53 – 53 N-linked (GlcNAc...) asparagine



Literature citations
SEMA3A, a gene involved in axonal pathfinding, is mutated in patients with Kallmann syndrome.
Hanchate N.K.; Giacobini P.; Lhuillier P.; Parkash J.; Espy C.; Fouveaut C.; Leroy C.; Baron S.; Campagne C.; Vanacker C.; Collier F.; Cruaud C.; Meyer V.; Garcia-Pinero A.; Dewailly D.; Cortet-Rudelli C.; Gersak K.; Metz C.; Chabrier G.; Pugeat M.; Young J.; Hardelin J.P.; Prevot V.; Dode C.;
PLoS Genet. 8:E1002896-E1002896(2012)
Cited for: VARIANTS HH16 TRP-66; SER-153; VAL-400; ILE-435; ALA-688; GLN-730 AND HIS-733; CHARACTERIZATION OF VARIANTS HH16 TRP-66; SER-153; VAL-400; ILE-435; ALA-688; GLN-730 AND HIS-733; The prevalence of CHD7 missense versus truncating mutations is higher in patients with Kallmann syndrome than in typical CHARGE patients.
Marcos S.; Sarfati J.; Leroy C.; Fouveaut C.; Parent P.; Metz C.; Wolczynski S.; Gerard M.; Bieth E.; Kurtz F.; Verier-Mine O.; Perrin L.; Archambeaud F.; Cabrol S.; Rodien P.; Hove H.; Prescott T.; Lacombe D.; Christin-Maitre S.; Touraine P.; Hieronimus S.; Dewailly D.; Young J.; Pugeat M.; Hardelin J.P.; Dode C.;
J. Clin. Endocrinol. Metab. 99:E2138-2143(2014)
Cited for: VARIANTS HH16 TRP-66; ARG-82; SER-153; THR-342; ILE-435; GLY-447; TRP-484; MET-657 AND GLN-730;
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.