UniProtKB/SwissProt variant VAR

Variant information

Variant position:

221

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 Cysteine (C) at position 221 (R221C, p.Arg221Cys).

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 (C)

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

BLOSUM score:

-3

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:

Many polymorphic variants of PGM1 exist. 8 different alleles are known: PGM1*1+, PGM1*1-, PGM1*2+, PGM1*2-, PGM1*3+, PGM1*3-, PGM1*7+ and PGM1*7-. The sequence of PGM1*1+ is shown here.

Additional information on the polymorphism described.

Variant description:

In allele PGM1*2+, allele PGM1*2-, allele PGM1*3+ and allele PGM1*3-; phosphoglucomutase activity is similar to wild-type.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs1126728 [ dbSNP | Ensembl ]

Sequence information

Variant position:

221

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

Protein sequence length:

562

The length of the canonical sequence.

Location on the sequence:

SIFDFSALKELLSGPNRLKI R IDAMHGVVGPYVKKILCEEL

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                         SIFDFSALKELLSGPNR---LKIRIDAMHGVVGPYVKKILCEEL

Mouse                         NIFDFNALKELLSGPNR---LKIRIDAMHGVVGPYVKKILC

Rat                           NIFDFNALKELLSGPNR---LKIRIDAMHGVVGPYVKKILC

Bovine                        NIFDFNALKELLSGPNR---LKIRIDAMHGVVGPYVKKILC

Rabbit                        NIFDFNALKELLSGPNR---LKIRIDAMHGVVGPYVKKILC

Slime mold                    TIFDFDGIRKFVKNHPN---FTFNFDAMSGVTGAYGKRIFT

Baker's yeast                 EIFDFDLIKSFLAKQRKDKGWKLLFDSLNGITGPYGKAIFV

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 – 562	Phosphoglucomutase-1
Modified residue	201 – 201	Phosphoserine
Modified residue	206 – 206	Phosphoserine
Modified residue	213 – 213	Phosphoserine
Beta strand	220 – 223

Literature citations

Cloning of human full-length CDSs in BD Creator(TM) system donor vector.
Kalnine N.; Chen X.; Rolfs A.; Halleck A.; Hines L.; Eisenstein S.; Koundinya M.; Raphael J.; Moreira D.; Kelley T.; LaBaer J.; Lin Y.; Phelan M.; Farmer A.;
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1); VARIANTS CYS-221 AND HIS-420;

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 CYS-221 AND HIS-420;

Intragenic recombination at the human phosphoglucomutase 1 locus: predictions fulfilled.
Takahashi N.; Neels J.V.;
Proc. Natl. Acad. Sci. U.S.A. 90:10725-10729(1993)
Cited for: VARIANTS MET-68; CYS-221 AND HIS-420;

The classical human phosphoglucomutase (PGM1) isozyme polymorphism is generated by intragenic recombination.
March R.E.; Putt W.; Hollyoake M.; Ives J.H.; Lovegrove J.U.; Hopkinson D.A.; Edwards Y.H.; Whitehouse D.B.;
Proc. Natl. Acad. Sci. U.S.A. 90:10730-10733(1993)
Cited for: VARIANTS CYS-221 AND HIS-420;

Compromised catalysis and potential folding defects in in vitro studies of missense mutants associated with hereditary phosphoglucomutase 1 deficiency.
Lee Y.; Stiers K.M.; Kain B.N.; Beamer L.J.;
J. Biol. Chem. 289:32010-32019(2014)
Cited for: CHARACTERIZATION OF VARIANTS CDG1T ALA-19; TYR-38; ARG-41; HIS-62; ALA-115; ARG-121; GLY-263; TYR-263; ARG-291; ARG-330; LYS-377; LYS-388 AND PRO-516; VARIANTS MET-68; CYS-221 AND HIS-420; CATALYTIC ACTIVITY; BIOPHYSICOCHEMICAL PROPERTIES; ACTIVE SITE; PHOSPHORYLATION AT SER-117; ACTIVITY REGULATION;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P36871: Variant p.Arg221Cys