UniProtKB/SwissProt variant VAR

Variant information

Variant position:

56

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

Type of variant:

US

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 Histidine (H) to Tyrosine (Y) at position 56 (H56Y, p.His56Tyr).

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 polar (H) to large size and aromatic (Y)

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 HIGM2; unknown pathological significance; loss of mutagenic activity.

Any additional useful information about the variant.

Sequence information

Variant position:

56

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

Protein sequence length:

198

The length of the canonical sequence.

Location on the sequence:

RDSATSFSLDFGYLRNKNGC H VELLFLRYISDWDLDPGRCY

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                         RDSATSFSLDFGYLRNKNGCHVELLFLRYISDWDLDPGRCY

                              RDSATSFSLDFGHLRNKSGCHVELLFLRYISDWDLDPGRCY

Mouse                         RDSATSCSLDFGHLRNKSGCHVELLFLRYISDWDLDPGRCY

Bovine                        RDSPTSFSLDFGHLRNKAGCHVELLFLRYISDWDLDPGRCY

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 – 198	Single-stranded DNA cytosine deaminase
Domain	23 – 129	CMP/dCMP-type deaminase
Active site	58 – 58	Proton donor
Metal binding	56 – 56	Zinc; catalytic
Modified residue	38 – 38	Phosphoserine; by PKA
Mutagenesis	38 – 38	S -> A. Loss of phosphorylation. Impaired class-switch recombination activity. No effect on interaction with CTNNBL1.
Mutagenesis	38 – 38	S -> D. No effect on interaction with CTNNBL1.
Mutagenesis	50 – 50	R -> G. Some reduced nuclear import; when associated with A-193.

Literature citations

Clinical, immunologic and genetic analysis of 29 patients with autosomal recessive hyper-IgM syndrome due to activation-induced cytidine deaminase deficiency.
Quartier P.; Bustamante J.; Sanal O.; Plebani A.; Debre M.; Deville A.; Litzman J.; Levy J.; Fermand J.P.; Lane P.; Horneff G.; Aksu G.; Yalcin I.; Davies G.; Tezcan I.; Ersoy F.; Catalan N.; Imai K.; Fischer A.; Durandy A.;
Clin. Immunol. 110:22-29(2004)
Cited for: VARIANTS HIGM2 TRP-24; TYR-56; ARG-80; ARG-87; PRO-106; VAL-139; SER-151 AND SER-174;

Activation induced cytidine deaminase mutant (AID-His130Pro) from Hyper IgM 2 patient retained mutagenic activity on SHM artificial substrate.
Ouadani H.; Ben-Mustapha I.; Ben-Ali M.; Largueche B.; Jovanic T.; Garcia S.; Arcangioli B.; Elloumi-Zghal H.; Fathallah D.; Hachicha M.; Masmoudi H.; Rougeon F.; Barbouche M.R.;
Mol. Immunol. 79:77-82(2016)
Cited for: CHARACTERIZATION OF VARIANTS HIGM2 TYR-56 AND PRO-130; FUNCTION;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9GZX7: Variant p.His56Tyr