Functional polymorphisms

What is the functional polymorphisms?
Polymorphisms that have been proven to influence gene functions are called functional polymorphisms. It is significant to know the distribution of functional polymorphisms in the rat, widely used in animal models for human diseases.

We assessed 19 functional polymorphisms consisting of 3 coat color and 16 disease-associated genes in 155 rat strains. To help research interests to select the most suitable strains for your experiments, NBRP-Rat will periodically improve and update the genetic profiles of rat strains.

Functional polymorphisms in inbred rat strains and their allele frequencies in commercially available outbred stocks.
Kuramoto T et al. Physiol Genomics. 2008 Apr 22;33(2):205-11.

The table of funnctional polymorphisims

Functional polymorphisms examined in this study. (Clicking Gene name jump to the each gene page provided by RGD.)

FPG ID* Causative Gene Phenotype Type of Mutation Reference
1 Asip
agouti Nonagouti (a) 19-bp deletion in exon 2 Kuramoto et al, 2001
2 Alb albumin Analbuminemia 7-bp deletion at splicing donor site in intron H Esumi et al, 1983
3 Cblb Cas-Br-M (murine) ecotropic retroviral transforming sequence b Insulin-dependent diabetes mellitus KDP QTL 1 Nonsense mutation at codon 455 (R455X) Yokoi et al, 2002
4 Cckar cholecystokinin A receptor Cholecystokinin A receptor 6.8-kb deletion spanning the promoter region, exon 1 and exon 2 Takiguchi et al, 1997
5 Cd36 CD36 molecule (thrombospondin receptor) QTL for insulin resistance, defective fatty acid metabolism and hypertriglyceridemia in SHR Deletion spanning the region between exon 4 of Cd36 and exon 5 of Cd36-ps2 Glazier et al, 2002
Gotoda et al, 1999
6 Cdkn1a cyclin-dependent kinase inhibitor 1A (p21, Cip1) Prostate cancer susceptibility 2 (Pcs2) 119-bp insertion in the promoter region Yamashita et al, 2005
7 Gja8
gap junction membrane channel protein alpha 8 UPL rat cataract (Uca) Missense mutation at codon 340 (R340W) Yamashita et al, 2002
8 Fcgr2a
Fc fragment of IgG, low affinity IIa, receptor (CD32) Crescentic glomerulonephritis 1 (Crgn1) Gene duplication Aitman et al, 2006
9 Fdft1 farnesyl diphosphate farnesyl transferase 1 Cataract SCR 2 (Cats2) Missense mutation at codon 196 (I196K) Mori et al, 2006
10 Prlhr
prolactin releasing hormone receptor Diabetes mellitus OLETF QTL 1 (Dmo1) Point mutation at translation initiation codon (M1I) Watanabe et al, 2005
11 Gimap5
GTPase, IMAP family member 5 Lymphopenia (Lyp) 1-bp Deletion resulting in frameshift MacMurray et al, 2002
12 Lss lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase) Cataract SCR 1 lethal (Cats1l) 12-bp deletion in exon 15 Mori et al, 2006
13 Lss lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase) Cataract SCR 1 (Cats1), Q481R Missense mutation at codon 481 (Q481R) Mori et al, 2006
14 Lss lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase) Cataract SCR 1 (Cats1), D139N Missense mutation at codon 139 (D139N) Mori et al, 2006
15 Oca2
oculocutaneous albinism 2 Pink-eyed dilution (p) Deletion spanning exon 17 and exon 18 Kuramoto et al, 2005
16 Rab38 RAB38, member RAS oncogene family Ruby (r) Point mutation at translation initiation codon (M1I) Oiso et al, 2004
17 Abcg5 ATP-binding cassette, sub-family G (WHITE), member 5 Phytosterolemia Missense mutation at codon 583 (G583C) Scoggan et al, 2003
18 Actr3
ARP3 actin-related protein 3 homolog (yeast) Albuminuria Missense mutation at codon 111 (L111F) Akiyama et al, 2007
19 Srebf1 sterol regulatory element binding transcription factor 1 Hepatic steatosis Point mutation at promoter region Pravenec et al, 2008
20 Dpp4 dipeptidylpeptidase 4 Deficiency in DPP4 serine proteinase Missense mutation at codon 633 (G633A) Tsuji et al, 1992
21 Hcn1 hyperpolarization-activated cyclic nucleotide-gated potassium channel 1 tremor behavior Missense mutation at codon 354 (A354V) Ohno et al, 2015
* Functional Polymorphism Gene ID