UniProtKB/Swiss-Prot P38398: Variant p.Ser1040Asn

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

1040 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 Serine (S) to Asparagine (N) at position 1040 (S1040N, p.Ser1040Asn). 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 polar (S) to medium size and polar (N) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

1 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 evidence that the presence of the rare form of Gln-356-Arg and Leu-871-Pro polymorphisms may be associated with an increased risk for developing ovarian cancer. Additional information on the polymorphism described.
Other resources:

Links to websites of interest for the variant.

Variant rs4986852 [ dbSNP | Ensembl ]

Sequence information Variant position:

1040 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:

PSTVSTISRNNIRENVFKEA S SSNINEVGSSTNEVGSSINE 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                         PSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINE

Gorilla                       PSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINE

                              QSTVSTISQNNIRECASKEVGSSSVNEVVSSTNEVGSSVNE

Rhesus macaque                PSTVSTISHNNIRENAFKEASSSNINEVGSSTNEVGSSINE

Chimpanzee                    PSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINE

Mouse                         QSTVHTVSLNN-RGNACQEAGS--------------GSIHE

Rat                           QSTIHTISLNN-RGDACLEASS--------------GSVIE

Bovine                        QSAVSTISQNNIQESTFKEVSSNSVNEVGSSTNEVGSSVNE

Caenorhabditis elegans        -----------------------------------------

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
Alternative sequence	64 – 1863	Missing. In isoform 2.
Alternative sequence	224 – 1365	Missing. In isoform 5.
Alternative sequence	264 – 1366	Missing. In isoform 3 and isoform 6.

Literature citations
Submission
NIEHS SNPs program;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS SER-275; ARG-356; ASN-693; LEU-871; GLY-1038; ASN-1040; GLY-1140; ARG-1183; GLY-1613 AND ALA-1620; Mutations in the BRCA1 gene in families with early-onset breast and ovarian cancer.
Castilla L.H.; Couch F.J.; Erdos M.R.; Hoskins K.F.; Calzone K.; Garber J.E.; Boyd J.; Lubin M.B.; Deshano M.L.; Brody L.C.; Collins F.S.; Weber B.L.;
Nat. Genet. 8:387-391(1994)
Cited for: VARIANT BC GLY-64; VARIANTS ALA-772; ASN-1040 AND GLY-1443; Confirmation of BRCA1 by analysis of germline mutations linked to breast and ovarian cancer in ten families.
Friedman L.S.; Ostermeyer E.A.; Szabo C.I.; Dowd P.; Lynch E.D.; Rowell S.E.; King M.-C.;
Nat. Genet. 8:399-404(1994)
Cited for: VARIANT BC GLY-61; VARIANTS ARG-356; GLY-1038; ASN-1040; ARG-1183 AND GLY-1613; Constant denaturant gel electrophoresis (CDGE) in BRCA1 mutation screening.
Andersen T.I.; Eiken H.G.; Couch F.; Kaada G.; Skrede M.; Johnsen H.; Aloysius T.A.; Tveit K.M.; Tranebjaerg L.; Doerum A.; Moeller P.; Weber B.L.; Boerresen-Dale A.-L.;
Hum. Mutat. 11:166-174(1998)
Cited for: VARIANT BC GLY-64; VARIANTS ALA-772; GLU-820; ASN-1040; GLY-1443; ILE-1512; LEU-1637 AND ILE-1652; BRCA1 and BRCA2 germline mutation spectrum and frequencies in Belgian breast/ovarian cancer families.
Claes K.; Poppe B.; Coene I.; De Paepe A.; Messiaen L.;
Br. J. Cancer 90:1244-1251(2004)
Cited for: VARIANTS ASN-693; ASN-1040; ALA-1060 AND MET-1665;

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.