UniProtKB/SwissProt variant VAR

Variant information

Variant position:

139

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 Arginine (R) to Histidine (H) at position 139 (R139H, p.Arg139His).

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 basic (R) to medium size and polar (H)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

0

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:

The HA-1H allele is presented on the cell surface and recognized by CTL, whereas the HA-1R allele is poorly represented by HLA-A and non-immunogenic, although HA-1R allelic frequency is the highest (PubMed:9820595, PubMed:16399573).

Additional information on the polymorphism described.

Variant description:

In allele HA-1H; induction of CTL recognition for epitope HA-1.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs1801284 [ dbSNP | Ensembl ]

Sequence information

Variant position:

139

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

Protein sequence length:

1136

The length of the canonical sequence.

Location on the sequence:

LLADVARFAEGLEKLKECVL R DDLLEARRPRAHECLGEALR

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                         LLADVARFAEGLEKLKECVLRDDLLEARRPRAHECLGEALR

Mouse                         LLADVARFAEGLEKLKECVLQDDLLEARRPLAHECLGEALR

Xenopus laevis                LLGDVARFAERLEKLRDVVQDEELKETRRPLAHECLGEALR

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 – 1136	Rho GTPase-activating protein 45
Peptide	137 – 145	Minor histocompatibility antigen HA-1

Literature citations

Submission
Mural R.J.; Istrail S.; Sutton G.G.; Florea L.; Halpern A.L.; Mobarry C.M.; Lippert R.; Walenz B.; Shatkay H.; Dew I.; Miller J.R.; Flanigan M.J.; Edwards N.J.; Bolanos R.; Fasulo D.; Halldorsson B.V.; Hannenhalli S.; Turner R.; Yooseph S.; Lu F.; Nusskern D.R.; Shue B.C.; Zheng X.H.; Zhong F.; Delcher A.L.; Huson D.H.; Kravitz S.A.; Mouchard L.; Reinert K.; Remington K.A.; Clark A.G.; Waterman M.S.; Eichler E.E.; Adams M.D.; Hunkapiller M.W.; Myers E.W.; Venter J.C.;
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]; VARIANTS HIS-139; ASP-259 AND GLY-439;

Genomic typing of minor histocompatibility antigen HA-1 by reference strand mediated conformation analysis (RSCA).
Arostegui J.I.; Gallardo D.; Rodriguez-Luaces M.; Querol S.; Madrigal J.A.; Garcia-Lopez J.; Granena A.;
Tissue Antigens 56:69-76(2000)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 82-140; VARIANT HIS-139;

Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes.
Graziano C.; Giorgi M.; Malentacchi C.; Mattiuz P.L.; Porfirio B.;
BMC Med. Genet. 6:36-36(2005)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 82-140; VARIANT HIS-139;

The minor histocompatibility antigen HA-1: a diallelic gene with a single amino acid polymorphism.
den Haan J.M.; Meadows L.M.; Wang W.; Pool J.; Blokland E.; Bishop T.L.; Reinhardus C.; Shabanowitz J.; Offringa R.; Hunt D.F.; Engelhard V.H.; Goulmy E.;
Science 279:1054-1057(1998)
Cited for: PROTEIN SEQUENCE OF 137-145; IDENTIFICATION BY MASS SPECTROMETRY; VARIANT HIS-139;

Definition of the gene encoding the minor histocompatibility antigen HA-1 and typing for HA-1 from genomic DNA.
Tseng L.-H.; Lin M.-T.; Martin P.J.; Pei J.; Smith A.G.; Hansen J.A.;
Tissue Antigens 52:305-311(1998)
Cited for: VARIANT HIS-139;

Therapeutic and diagnostic applications of minor histocompatibility antigen HA-1 and HA-2 disparities in allogeneic hematopoietic stem cell transplantation: a survey of different populations.
Di Terlizzi S.; Zino E.; Mazzi B.; Magnani C.; Tresoldi C.; Perna S.K.; Bregni M.; Rossini S.; Ciceri F.; Bordignon C.; Bonini C.; Fleischhauer K.;
Biol. Blood Marrow Transplant. 12:95-101(2006)
Cited for: VARIANT HIS-139;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q92619: Variant p.Arg139His