UniProtKB/Swiss-Prot P39060: Variant p.Val1076Ile

Collagen alpha-1(XVIII) chain
Gene: COL18A1
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Variant information Variant position:

1076 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 Valine (V) to Isoleucine (I) at position 1076 (V1076I, p.Val1076Ile). 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
Polymorphism:

There is an association between a polymorphism in position 1675 and prostate cancer. Heterozygous Asn-1675 individuals have a 2.5 times increased chance of developing prostate cancer as compared with homozygous Asp-1675 individuals. Additional information on the polymorphism described.
Other resources:

Links to websites of interest for the variant.

Variant rs62000962 [ dbSNP | Ensembl ]

Sequence information Variant position:

1076 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

1754 The length of the canonical sequence.
Location on the sequence:

KGDPGVPGLPGAKGEVGADG V PGFPGLPGREGIAGPQGPKG 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                         KGDPGVPGLPGAKGEVGADGVPGFPGLPGREGIAGPQGPKG

Mouse                         KGDPGVAGLPGAKGEVGADGAQGIPGPPGREGAAGSPGPKG

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	24 – 1754	Collagen alpha-1(XVIII) chain
Region	645 – 1443	Disordered
Region	1045 – 1127	Triple-helical region 4 (COL4)

Literature citations
Complete primary structure of two variant forms of human type XVIII collagen and tissue-specific differences in the expression of the corresponding transcripts.
Saarela J.; Ylikarppa R.; Rehn M.; Purmonen S.; Pihlajaniemi T.;
Matrix Biol. 16:319-328(1998)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 2 AND 3); VARIANT ILE-1076; Characterization of the human type XVIII collagen gene and proteolytic processing and tissue location of the variant containing a frizzled motif.
Elamaa H.; Snellman A.; Rehn M.; Autio-Harmainen H.; Pihlajaniemi T.;
Matrix Biol. 22:427-442(2003)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS 1; 2 AND 3); VARIANTS ILE-1076 AND ASN-1675; 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 3); VARIANT ILE-1076; A polymorphism in endostatin, an angiogenesis inhibitor, predisposes for the development of prostatic adenocarcinoma.
Iughetti P.; Suzuki O.; Godoi P.H.; Alves V.A.; Sertie A.L.; Zorick T.; Soares F.; Camargo A.A.; Moreira E.S.; di Loreto C.; Moreira-Filho C.A.; Simpson A.; Oliva G.; Passos-Bueno M.R.;
Cancer Res. 61:7375-7378(2001)
Cited for: VARIANTS ILE-1076 AND ASN-1675; Knobloch syndrome: novel mutations in COL18A1, evidence for genetic heterogeneity, and a functionally impaired polymorphism in endostatin.
Menzel O.; Bekkeheien R.C.J.; Reymond A.; Fukai N.; Boye E.; Kosztolanyi G.; Aftimos S.; Deutsch S.; Scott H.S.; Olsen B.R.; Antonarakis S.E.; Guipponi M.;
Hum. Mutat. 23:77-84(2004)
Cited for: VARIANTS LEU-49; ARG-111; ILE-1076 AND ARG-1121; CHARACTERIZATION OF VARIANT ASN-1675;

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.