rs249954, also known as 2586+58C>T, is an intronic SNP in the PALB2 gene.

There is conflicting literature about the association of this SNP with increased risk for breast cancer, but overall, it seems as if any association between rs249954 and breast cancer is likely to be either nonexistent or at least fairly small. Specifically:

  • ClinVar tags this SNP as benign, based on a single submission
  • A 2008 study of 1,000 Chinese with breast cancer reports a 36% increase in breast cancer risk (odds ratio 1.36, CI: 1.13-1.64, p = 0.001; TT/TC versus CC genotypes)[PMID 1879410]
  • A 2010 study of 660 Chinese patients did not find an association for this SNP [PMID 19921424]
  • A 2010 study of Polish patients reported an allele frequency of 5.7% (4 out of 70) in those patients but did not report the frequency in matched controls [PMID 20122277]
  • A 2013 study of ~100 (male) Spanish patients reports no difference in allele frequency between patients and controls[PMID 23935836]

[PMID 19921424] Five common single nucleotide polymorphisms in the PALB2 gene and susceptibility to breast cancer in eastern Chinese population



[PMID 18794107] Association of common PALB2 polymorphisms with breast cancer risk: a case-control study.

[PMID 20122277] A novel germline PALB2 deletion in Polish breast and ovarian cancer patients.

rs249954

Parent Gene: PALB2

Importance: 3
Less common allele: A = 35%
More common allele: G = 65%
My Genotype: Log In
Risk Allele: A

Disease/Trait: Schizophrenia

The A allele of rs249954 is reported to be associated with Schizophrenia (R) . Your genotype was not identified for this SNP so we are unable to comment on your association with Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined) (Modelling analysis).

Disease/Trait: Bipolar Disorder

The A allele of rs249954 is reported to be associated with Bipolar Disorder (R) . Your genotype was not identified for this SNP so we are unable to comment on your association with Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined) (Modelling analysis).

Disease/Trait: Attention Deficit Hyperactivity Disorder

The A allele of rs249954 is reported to be associated with Attention Deficit Hyperactivity Disorder (R) . Your genotype was not identified for this SNP so we are unable to comment on your association with Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined) (Modelling analysis).

Disease/Trait: Unipolar Depression

The A allele of rs249954 is reported to be associated with Unipolar Depression (R) . Your genotype was not identified for this SNP so we are unable to comment on your association with Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined) (Modelling analysis).

Disease/Trait: Autism Spectrum Disorder

The A allele of rs249954 is reported to be associated with Autism Spectrum Disorder (R) . Your genotype was not identified for this SNP so we are unable to comment on your association with Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined) (Modelling analysis).