UniProtKB/Swiss-Prot P08572: Variant p.Ala1690Thr

Collagen alpha-2(IV) chain
Gene: COL4A2
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Variant information Variant position:

1690 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 1690 (A1690T, p.Ala1690Thr). 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
Variant description:

Risk factor for ICH; results in a significantly decreased extracellular-to-intracellular ratio of COL4A2 and COL4A1 proteins, indicating interference with the proper secretion of both these proteins. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs201105747 [ dbSNP | Ensembl ]

Sequence information Variant position:

1690 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

1712 The length of the canonical sequence.
Location on the sequence:

NKYSFWLTTIPEQSFQGSPS A DTLKAGLIRTHISRCQVCMK 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                         NKYSFWLTTIPEQSFQGSPSADTLKAGLIRTHISRCQVCMK

Mouse                         NKYSFWLTTIPEQNFQSTPSADTLKAGLIRTHISRCQVCMK

Caenorhabditis elegans        NKFSFWLTTIDNDSEFKVPESQTLKSGNLRTRVSRCQVCVK

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	184 – 1712	Collagen alpha-2(IV) chain
Chain	1486 – 1712	Canstatin
Domain	1489 – 1712	Collagen IV NC1
Disulfide bond	1612 – 1708
Disulfide bond	1646 – 1705

Literature citations
COL4A2 mutations impair COL4A1 and COL4A2 secretion and cause hemorrhagic stroke.
Jeanne M.; Labelle-Dumais C.; Jorgensen J.; Kauffman W.B.; Mancini G.M.; Favor J.; Valant V.; Greenberg S.M.; Rosand J.; Gould D.B.;
Am. J. Hum. Genet. 90:91-101(2012)
Cited for: INVOLVEMENT IN SUSCEPTIBILITY TO ICH; VARIANTS PHE-192; LYS-517; ALA-683; ARG-701; SER-718; GLN-1109; GLY-1123; LYS-1150; ILE-1399 AND THR-1690; CHARACTERIZATION OF VARIANTS GLY-1123; LYS-1150 AND THR-1690;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.