UniProtKB/Swiss-Prot Q9Y4P1: Variant p.Leu354Gln

Cysteine protease ATG4B
Gene: ATG4B
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Variant information Variant position:

354 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant:

LB/B 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 Glutamine (Q) at position 354 (L354Q, p.Leu354Gln). 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 medium size and polar (Q) 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
Other resources:

Links to websites of interest for the variant.

Variant rs7601000 [ dbSNP | Ensembl ]

Sequence information Variant position:

354 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

393 The length of the canonical sequence.
Location on the sequence:

QQVKKLSLLGGALPMFELVE L QPSHLACPDVLNLSLDSSDV 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                         QQVKKLSLLGGALPMFELVELQPSHLACPDVLNLSLDSSDV

Mouse                         QQVKKLSQLGGALPMFELVEQQPSHLACQDVLNLSLDSSDV

Rat                           QQVKKLSQLGGALPMFELVEQQPSHLACQDVLNLSLDSSDV

Bovine                        QQVSKLSLLGGALPMFELVEQQPSHLACPDVLNLSLDSSDA

Chicken                       HQIKKLSLVRGALPMFELVERQPSHFSNPDVLNLTPDSSDA

Xenopus laevis                QHIKKLSLSGGALPMFEVVDQLPLHLSNPDVLNLTPDSSDA

Zebrafish                     AQIRKVSNCRG-LPMFELVDSQPSHLITADVLNLTPDFSDS

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.

Type	Positions	Description
Chain	1 – 393	Cysteine protease ATG4B
Disulfide bond	292 – 361
Disulfide bond	361 – 361	Interchain (with C-292)
Alternative sequence	321 – 354	FFCKTEDDFNDWCQQVKKLSLLGGALPMFELVEL -> KQGRLVRSLIPWAPRPSSWCAAVLGAAVVMCGTP. In isoform 3.
Alternative sequence	369 – 369	L -> LGESCQVQVGSLG. In isoform 4.
Mutagenesis	361 – 361	C -> S. Reduced formation of intrachain and interchain disulfide bonds in response to oxidation. Abolished formation of disulfide bonds, leading to increased autophagy; when associated with S-292.

Literature citations
LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation.
Kabeya Y.; Mizushima N.; Yamamoto A.; Oshitani-Okamoto S.; Ohsumi Y.; Yoshimori T.;
J. Cell Sci. 117:2805-2812(2004)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); FUNCTION IN GABARAPL2; GABARAP AND MAP1LC3A CLEAVAGE; ACTIVE SITE; MUTAGENESIS OF CYS-74; VARIANT GLN-354; Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.
Nagase T.; Ishikawa K.; Suyama M.; Kikuno R.; Hirosawa M.; Miyajima N.; Tanaka A.; Kotani H.; Nomura N.; Ohara O.;
DNA Res. 6:63-70(1999)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1); VARIANT GLN-354; The full-ORF clone resource of the German cDNA consortium.
Bechtel S.; Rosenfelder H.; Duda A.; Schmidt C.P.; Ernst U.; Wellenreuther R.; Mehrle A.; Schuster C.; Bahr A.; Bloecker H.; Heubner D.; Hoerlein A.; Michel G.; Wedler H.; Koehrer K.; Ottenwaelder B.; Poustka A.; Wiemann S.; Schupp I.;
BMC Genomics 8:399-399(2007)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1); VARIANT GLN-354; The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
The MGC Project Team;
Genome Res. 14:2121-2127(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1); VARIANT GLN-354;

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.