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UniProtKB/Swiss-Prot Q15904: Variant p.Tyr313Cys

V-type proton ATPase subunit S1
Gene: ATP6AP1
Variant information

Variant position:  313
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 Tyrosine (Y) to Cysteine (C) at position 313 (Y313C, p.Tyr313Cys).
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 aromatic (Y) to medium size and polar (C)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -2
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 IMD47; probable loss of proton-transporting V-type ATPase complex assembly in yeast; unable to restore V-ATPase-dependent growth in Voa1 mutant yeast.
Any additional useful information about the variant.

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



Sequence information

Variant position:  313
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  470
The length of the canonical sequence.

Location on the sequence:   QELNLTGSFWNDSFARLSLT  Y ERLFGTTVTFKFILANRLYP
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                         QELNLTGSFWNDSFARLSLTYE-RLFGTTVTFKFILANRLYP

Mouse                         ENLNLTGSFWNDSFAMLSLTYE-PLFGATVTFKFILASRFY

Rat                           ENLNLTGSFWNDSFAMLSLTYE-PLFGATVTFKFILASRFY

Bovine                        QDLNLTGSFWNDTVARLVLTYD-SLFGTMVTFKFILANSYY

Drosophila                    TDLKLT----NSSSTKLSVVMDTSVADKPITFDVVYNGGY-

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 42 – 470 V-type proton ATPase subunit S1
Topological domain 42 – 419 Vacuolar
Glycosylation 296 – 296 N-linked (GlcNAc...) asparagine
Glycosylation 303 – 303 N-linked (GlcNAc...) asparagine


Literature citations

ATP6AP1 deficiency causes an immunodeficiency with hepatopathy, cognitive impairment and abnormal protein glycosylation.
Jansen E.J.; Timal S.; Ryan M.; Ashikov A.; van Scherpenzeel M.; Graham L.A.; Mandel H.; Hoischen A.; Iancu T.C.; Raymond K.; Steenbergen G.; Gilissen C.; Huijben K.; van Bakel N.H.; Maeda Y.; Rodenburg R.J.; Adamowicz M.; Crushell E.; Koenen H.; Adams D.; Vodopiutz J.; Greber-Platzer S.; Mueller T.; Dueckers G.; Morava E.; Sykut-Cegielska J.; Martens G.J.; Wevers R.A.; Niehues T.; Huynen M.A.; Veltman J.A.; Stevens T.H.; Lefeber D.J.;
Nat. Commun. 7:11600-11600(2016)
Cited for: INVOLVEMENT IN IMD47; VARIANTS IMD47 PRO-144; CYS-313; LYS-346 AND ILE-428; CHARACTERIZATION OF VARIANTS IMD47 CYS-313; LYS-346 AND ILE-428; SUBCELLULAR LOCATION; TISSUE SPECIFICITY; GLYCOSYLATION; MUTAGENESIS OF VAL-470;

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.