UniProtKB/SwissProt variant VAR

Variant information

Variant position:

34

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

Type of variant:

LP/P [Disclaimer]

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 Leucine (L) to Proline (P) at position 34 (L34P, p.Leu34Pro).

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 hydrophobic.

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

Variant description:

In GPIBD18; partial loss of function; when tested in PIGS-knockout cells, mediates partial restoration of GPI-anchored protein expression at the cell surface.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs1567618413 [ dbSNP | Ensembl ]

Sequence information

Variant position:

34

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

Protein sequence length:

555

The length of the canonical sequence.

Location on the sequence:

ARGKRAALFFAAVAIVLGLP L WWKTTETYRASLPYSQISGL

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                         ARG-----------KRAALFFAAVAIVLGLPLWWKTTETYRASLPYSQISGL

Mouse                         VRG-----------KRSALFFAAVAILLGLPLWWKTTETYR

Rat                           VRG-----------KRAALFFAAVAILLGLPLWWKTTETYR

Bovine                        VRG-----------KRAALFFATVVIVLGLPLWWKTTETYR

Fission yeast                 ERSNFQLNKPEKSLKRYALLSFYVIILLAIPVWWKTTHYER

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	2 – 555	GPI transamidase component PIG-S
Transmembrane	19 – 39	Helical

Literature citations

Mutations in PIGS, encoding a GPI transamidase, cause a neurological syndrome ranging from fetal akinesia to epileptic encephalopathy.
Nguyen T.T.M.; Murakami Y.; Wigby K.M.; Baratang N.V.; Rousseau J.; St-Denis A.; Rosenfeld J.A.; Laniewski S.C.; Jones J.; Iglesias A.D.; Jones M.C.; Masser-Frye D.; Scheuerle A.E.; Perry D.L.; Taft R.J.; Le Deist F.; Thompson M.; Kinoshita T.; Campeau P.M.;
Am. J. Hum. Genet. 103:602-611(2018)
Cited for: INVOLVEMENT IN GPIBD18; VARIANTS GPIBD18 PRO-34; 36-TRP--ASP-555 DEL; GLY-308 AND 439-THR--LYS-451 DELINS ARG-LEU-LEU; PATHWAY; FUNCTION;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q96S52: Variant p.Leu34Pro