UniProtKB/Swiss-Prot P38398: Variant p.Leu1780Pro

Breast cancer type 1 susceptibility protein
Gene: BRCA1
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Variant information Variant position:

1780 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant:

US 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 1780 (L1780P, p.Leu1780Pro). 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 BC, BROVCA1 and OC; uncertain significance. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs80357474 [ dbSNP | Ensembl ]

Sequence information Variant position:

1780 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

1863 The length of the canonical sequence.
Location on the sequence:

IFRGLEICCYGPFTNMPTDQ L EWMVQLCGASVVKELSSFTL 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                         IFRGLEICCYGPFTNMPTDQLEWMVQL---CGASVVKELSSFTL

Gorilla                       IFRGLDICCYGPFTNMPTDQLEWMVQL---CGASVVKELSS

                              IFRGLEICCYGPFTNMPTDQLEWMVHL---CGASVVKEPSL

Rhesus macaque                IFRGLEICCYGPFTNMPTDQLEWMVQL---CGASVVKELSS

Chimpanzee                    IFRGLEICCYGPFTNMPTDQLEWMVQL---CGASVVKELSS

Mouse                         LFKGLQVYCCEPFTNMPKDELERMLQL---CGASVVKELPS

Rat                           LFEGLQIYCCEPFTNMPKDELERMLQL---CGASVVKELPL

Bovine                        IFKGLEICCYGPFTNMPTDQLEWMVQL---CGASVVKEPSS

Caenorhabditis elegans        LFAGRRFMILRKFTMNPYFDYKQLIELVQQCGGEILSCYEN

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 – 1863	Breast cancer type 1 susceptibility protein
Domain	1756 – 1855	BRCT 2
Alternative sequence	64 – 1863	Missing. In isoform 2.
Alternative sequence	1778 – 1863	DQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY -> GCPPNCGCAARCLDRGQWLPCNWADV. In isoform 6.
Helix	1777 – 1786

Literature citations
Suggestion of BRCA1 c.5339T>C (p.L1780P) variant confer from 'unknown significance' to 'Likely pathogenic' based on clinical evidence in Korea.
Ryu J.M.; Kang G.; Nam S.J.; Kim S.W.; Yu J.; Lee S.K.; Bae S.Y.; Park S.; Paik H.J.; Kim J.W.; Park S.S.; Lee J.E.; Kim S.W.;
Breast 33:109-116(2017)
Cited for: VARIANT BC PRO-1780; VARIANT BROVCA1 PRO-1780; VARIANT OC PRO-1780;

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.