UniProtKB/Swiss-Prot P0C870: Variant p.Met160Val

Bifunctional peptidase and (3S)-lysyl hydroxylase JMJD7
Gene: JMJD7
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Variant information Variant position:

160 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 Methionine (M) to Valine (V) at position 160 (M160V, p.Met160Val). 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:

Similar physico-chemical property. Both residues are medium size and hydrophobic. The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

1 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

Sequence information Variant position:

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

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

PQLLPDLESHVPWASEALGK M PDAVNFWLGEAAAVTSLHKD 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                         PQLLPDLESHVPWASEALGKMPDAVNFWLGEAAAVTSLHKD

Mouse                         PQLLSDIESHVPWASESLGKMPDAVNFWLGDASAVTSLHKD

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 – 316	Bifunctional peptidase and (3S)-lysyl hydroxylase JMJD7
Domain	128 – 307	JmjC
Binding site	178 – 178
Binding site	180 – 180
Mutagenesis	178 – 178	H -> A. Loss of peptidase activity toward methylated histones and reduced anchorage-independent growth of transformed cells; when associated with A-180 and A-277. Impairs L-lysine (3S)-hydroxylase activity. Impairs the interaction with DRG1 and DRG2.
Mutagenesis	180 – 180	D -> A. Loss of peptidase activity toward methylated histones and reduced anchorage-independent growth of transformed cells; when associated with A-180 and A-277.

Literature citations
Diagnostic exome sequencing in persons with severe intellectual disability.
de Ligt J.; Willemsen M.H.; van Bon B.W.; Kleefstra T.; Yntema H.G.; Kroes T.; Vulto-van Silfhout A.T.; Koolen D.A.; de Vries P.; Gilissen C.; del Rosario M.; Hoischen A.; Scheffer H.; de Vries B.B.; Brunner H.G.; Veltman J.A.; Vissers L.E.;
N. Engl. J. Med. 367:1921-1929(2012)
Cited for: VARIANT VAL-160;

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.