UniProtKB/SwissProt variant VAR

Variant information

Variant position:

348

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 Alanine (A) to Threonine (T) at position 348 (A348T, p.Ala348Thr).

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 small size and hydrophobic (A) to medium size and polar (T)

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:

There is a significant association between the variants Ala-3, Leu-251 and Thr-348 and a low expression of CD177 on neutrophils (PubMed:12623849, PubMed:14692971). Expression of CD177 on neutrophils is a trait determined by ratio of CD177/CD177P1 alleles (PubMed:27227454). The phenotype of CD177 null neutrophils is due to recombination between exon 7 of CD177 and the pseudogene CD177P1 through gene conversion, changing Lys-263 codon into stop codon (PubMed:27227454). The lack of CD177 expression affects 1-10 percent of the population placing them at risk for formation of anti-neutrophil antibodies that can cause transfusion-related acute lung injury and neonatal alloimmune neutropenia.

Additional information on the polymorphism described.

Other resources:

Links to websites of interest for the variant.

Variant rs17856829 [ dbSNP | Ensembl ]

Sequence information

Variant position:

348

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

Protein sequence length:

437

The length of the canonical sequence.

Location on the sequence:

CVQPLGTCSSGSPRMTCPRG A THCYDGYIHLSGGGLSTKMS

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                         CVQPLGTCSSGSPRMTCPRGATHCYDGYIHLSGGGLSTKMS

Mouse                         CVELFGSCKS-TDSVTCPRGATHCYKGDIALQGGGLTTRVS

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	22 – 408	CD177 antigen
Domain	325 – 377	UPAR/Ly6 2
Alternative sequence	146 – 437	Missing. In isoform 3.
Alternative sequence	249 – 437	Missing. In isoform 2.

Literature citations

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); VARIANTS PRO-3 AND THR-348;

Lack of NB1 GP (CD177/HNA-2a) gene transcription in NB1 GP-neutrophils from NB1 GP-expressing individuals and association of low expression with NB1 gene polymorphisms.
Wolff J.; Brendel C.; Fink L.; Bohle R.M.; Kissel K.; Bux J.;
Blood 102:731-733(2003)
Cited for: VARIANT THR-348; POLYMORPHISM;

Heterogeneity of human neutrophil CD177 expression results from CD177P1 pseudogene conversion.
Wu Z.; Liang R.; Ohnesorg T.; Cho V.; Lam W.; Abhayaratna W.P.; Gatenby P.A.; Perera C.; Zhang Y.; Whittle B.; Sinclair A.; Goodnow C.C.; Field M.; Andrews T.D.; Cook M.C.;
PLoS Genet. 12:E1006067-E1006067(2016)
Cited for: VARIANTS PRO-3; LEU-31; ILE-251; ALA-261; THR-348 AND ARG-431; SUBCELLULAR LOCATION; TISSUE SPECIFICITY; POLYMORPHISM;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q8N6Q3: Variant p.Ala348Thr