UniProtKB/Swiss-Prot Q86YC2: Variant p.Tyr28Cys

Partner and localizer of BRCA2
Gene: PALB2
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Variant information Variant position:

28 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 Tyrosine (Y) to Cysteine (C) at position 28 (Y28C, p.Tyr28Cys). 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 large size and aromatic (Y) to medium size and polar (C) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

-2 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:

Abrogates the interaction with BRCA1; decreases double-stranded DNA break-initiated homologous recombination; reduces PALB2 and RAD51 localization to ionizing radiation-induced foci; may weaken homooligomerization. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs515726129 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

1186 The length of the canonical sequence.
Location on the sequence:

PLSCEEKEKLKEKLAFLKRE Y SKTLARLQRAQRAEKIKHSI 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                         PLSCEEKEKLKEKLAFLKREYSKTLARLQRAQRAEKIKHSI

Mouse                         PLSYAEKEKLKEKLAFLKKEYSRTLARLQRAKRAEKAKNS-

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 – 1186	Partner and localizer of BRCA2
Region	1 – 579	DNA-binding (with the preference D loop > dsDNA > ssDNA)
Region	1 – 319	Interaction with BRCA1
Region	1 – 200	Interaction with RAD51
Region	1 – 160	Required for its oligomerization and is important for its focal concentration at DNA damage sites
Coiled coil	9 – 41
Mutagenesis	14 – 14	K -> A. Loss of interaction with BRCA1 but no effect on interaction with BRCA2.
Mutagenesis	21 – 21	L -> A. Loss of interaction with BRCA1 but no effect on interaction with BRCA2.
Mutagenesis	28 – 28	Y -> A. Loss of interaction with BRCA1 but no effect on interaction with BRCA2.
Mutagenesis	35 – 35	L -> A. Loss of interaction with BRCA1 but no effect on interaction with BRCA2.
Mutagenesis	42 – 42	E -> A. Loss of interaction with BRCA1 but no effect on interaction with BRCA2.

Literature citations
Compromised BRCA1-PALB2 interaction is associated with breast cancer risk.
Foo T.K.; Tischkowitz M.; Simhadri S.; Boshari T.; Zayed N.; Burke K.A.; Berman S.H.; Blecua P.; Riaz N.; Huo Y.; Ding Y.C.; Neuhausen S.L.; Weigelt B.; Reis-Filho J.S.; Foulkes W.D.; Xia B.;
Oncogene 36:4161-4170(2017)
Cited for: FUNCTION; SUBUNIT; INTERACTION WITH BRCA1; BRCA2 AND RAD51; SUBCELLULAR LOCATION; VARIANT PRO-35; CHARACTERIZATION OF VARIANT PRO-35; CHARACTERIZATION OF VARIANTS ARG-18; CYS-28 AND HIS-37;

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.