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UniProtKB/Swiss-Prot Q96T83: Variant p.Leu515Phe

Sodium/hydrogen exchanger 7
Gene: SLC9A7
Variant information

Variant position:  515
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 Leucine (L) to Phenylalanine (F) at position 515 (L515F, p.Leu515Phe).
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 medium size and hydrophobic (L) to large size and aromatic (F)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  0
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 MRX108; probable gain-of-function variant; affects the regulation of trans-Golgi network/post-Golgi pH homeostasis, causing alkalinization of these compartments compared to wild-type, hence affecting its own glycosylation and that of exported cargo proteins; no effect on subcellular location in the Golgi apparatus and plasma membrane.
Any additional useful information about the variant.



Sequence information

Variant position:  515
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  725
The length of the canonical sequence.

Location on the sequence:   ALAIRDTASYARQMMFTTTL  L IVFFTVWIIGGGTTPMLSWL
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                         ALAIRDTASYARQMMFTTTLLIVFFTVWIIGGGTTPMLSWL

Mouse                         ALAIRDTASYARQMMFTTTLLIVFFTVWVIGGGTTPMLSWL

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 1 – 725 Sodium/hydrogen exchanger 7
Transmembrane 514 – 534 Helical


Literature citations

A recurrent missense variant in SLC9A7 causes nonsyndromic X-linked intellectual disability with alteration of Golgi acidification and aberrant glycosylation.
Khayat W.; Hackett A.; Shaw M.; Ilie A.; Dudding-Byth T.; Kalscheuer V.M.; Christie L.; Corbett M.A.; Juusola J.; Friend K.L.; Kirmse B.M.; Gecz J.; Field M.; Orlowski J.;
Hum. Mol. Genet. 28:598-614(2019)
Cited for: INVOLVEMENT IN MRX108; VARIANT MRX108 PHE-515; CHARACTERIZATION OF VARIANT MRX108 PHE-515; FUNCTION; GLYCOSYLATION AT ASN-145; SUBCELLULAR LOCATION; TOPOLOGY;

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.