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UniProtKB/Swiss-Prot Q9NQV7: Variant p.Asn790His

Histone-lysine N-methyltransferase PRDM9
Gene: PRDM9
Variant information

Variant position:  790
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 Asparagine (N) to Histidine (H) at position 790 (N790H, p.Asn790His).
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 polar.
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

Polymorphism:  Several alleles exist depending on both the number of zinc finger C2H2 type domains and their identity (PubMed:26833727). Each allele binds to a specific hotspot set (PubMed:26833727). Variations in the zinc finger C2H2 type domains are associated with significant differences in affinity towards DNA-binding motif (PubMed:26833727). The sequence shown is that of allele B.
Additional information on the polymorphism described.

Variant description:  In allele L20; reduces affinity for the DNA-binding motif 5?-GCCTCCCTAGCCACG-3'.
Any additional useful information about the variant.

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



Sequence information

Variant position:  790
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  894
The length of the canonical sequence.

Location on the sequence:   HTGEKPYVCRECGRGFRDKS  N LLSHQRTHTGEKPYVCRECG
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                         HTGEKPYVCRECGRGFRDKSNLLSHQRTHTGEKPYVCRECG

Mouse                         HTGEKPYVCRECGRGFTAKSVLIQHQRTHTGEKPYVCRECG

Rat                           HTGEKPYICRECGRGFT------------------------

Zebrafish                     HTGEKPYTCSQCGKSFVHSGQLNVHLRTHTGEKPFLCSQCG

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 – 894 Histone-lysine N-methyltransferase PRDM9
Zinc finger 776 – 798 C2H2-type 11
Region 730 – 820 DNA-binding
Metal binding 770 – 770 Zinc 4; via tele nitrogen
Metal binding 778 – 778 Zinc 5
Metal binding 781 – 781 Zinc 5
Metal binding 794 – 794 Zinc 5; via tele nitrogen
Metal binding 798 – 798 Zinc 5; via tele nitrogen
Metal binding 806 – 806 Zinc 6
Metal binding 809 – 809 Zinc 6
Helix 788 – 799


Literature citations

No reference for the current variant in UniProtKB/Swiss-Prot.

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.