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Table 3 Genes and non-synonymous variations in LH vs LN haplotype blocks on RNO17

From: Genomic structure of nucleotide diversity among Lyon rat models of metabolic syndrome

Gene name Gene start (bp) Gene end (bp) Description Nucleotide Substitution AA Substitution Variant strain Classification
Block 1 (29.7-30 Mb)
Tmem14c 29,701,923 29,708,044 Transmembrane protein 14C     
Pak1ip2 29,710,407 29,721,477 PAK1 interacting protein 1     
RGD1562963 29,733,271 29,746,769 Similar to chromosome 6 open reading frame 52 G29,733,378A V36I LH Benign
G29,741,903A R135H Benign
G29,741,915A C139Y Benign
Gcnt2 29,767,388 29,872,873 N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase C29,872,483 T A131T LN Benign
Block 2 (30.1-30. Mb)
LOC100362620 30,267,398 30,267,637 CDC28 protein kinase regulatory subunit 2 G30,267,440A E15K LN Benign
T30,267,495C L33P Benign
G30,267,526C W43C Benign
G30,267,578 T E61* N/A
Block 5 (41.7-43.1 Mb)
RGD1563300 42,228,845 42,229,431 Similar to 60S ribosomal protein L29 (P23) g.42299020_42299027delACTCCGGT   LH Essential splice site
g.42299028_42299029insCACAAAGATA X29fs LN Frameshift
Prl5a2 42,984,939 42,991,275 Prolactin family 5, subfamily a, member 2 G42,989,474A P14L LH Benign
A42,986,191 T   LH Splice site
Block 6 (43.2-43.4 Mb)
Prl5a1 43,119,152 43,126,570 Prolactin-5A1     
Prl4a1 43,276,214 43,284,152 Prolactin-4A1 G43,278,266 T T141N LH Splice site, possibly damaging
Block 7 (53.4-53.8 Mb)
Stard3nl 53,402,078 53,436,081 MLN64 N-terminal domain homolog     
ENSRNOG00000027571 53,441,303 53,484,317 Uncharacterized protein G53,441,394A T161I /T313I* LH Benign
C53,463,467 T V124I LH
g.53483901_53483997del 73_105del LN Frameshift
ENSRNOG00000012418 53,496,423 53,528,130 Uncharacterized protein G53,527,707 T P81T LH Possibly damaging
T53,527,779A T57S LH Benign
G53,528,005A P15S LH Probably damaging
G53,528,025 T A8D LH Possibly damaging
Amph 53,558,804 53,802,936 Amphiphysin C53,558,811A R632L LH Benign
g.53641892_53641893delCT c.152_153delAG LN  
ENSRNOG00000038737 53,773,036 53,773,733 Uncharacterized protein     
Block 8 (62.2-63.2 Mb)
Bambi 62,654,080 62,658,885 BMP and activin membrane-bound inhibitor homolog     
RGD1564129 62,684,244 62,686,747 Uncharacterized protein     
Cul2 62,701,289 62,741,344 Cullin-2     
Crem 62,770,633 62,837,668 cAMP-responsive element modulator     
Epc1 63,041,415 63,104,046 Enhancer of polycomb homolog 1 A63,102,600 T L55H LH Benign
Block 9 (63.4-64.9 Mb)
Rab18 63,497,924 63,529,227 Ras-related protein Rab-18 A63,528,108 T S193C LN Benign
Mkx 63,631,426 63,710,099 Mohawk Homeobox G63,631,814A P301L LH Benign
Armc4 63,931,393 63,955,410 Armadillo repeat containing 4     
Mpp7 63,992,387 64,282,554 MAGUK p55 subfamily member 7     
Wac 64,531,772 64,587,027 WW domain containing adaptor with coiled-coil T64,570,567G C200G LH Benign
Block 10 (65.0-65.9 Mb)
LOC364753 65,681,793 65,702,382 similar to NSFL1 (p97) cofactor (p47) G65,701,876 T G80C LH Possibly damaging
Block 13 (83.6-83.9 Mb)
ENSRNOG00000031981 83,837,499 83,861,361 Uncharacterized protein C83,860,804 T P40S LH Benign
g.83861107_83861122delATCCCTGCATCCCTGC I141fs LN Frameshift
g.83861220_83861227delCCCTGCAT T178fs LH Frameshift
g.83837957_83837958insA   LH Splice site
Block 14 (90.8-91.1 Mb)
Plxdc2 90,572,391 90,982,073 Plexin domain-containing protein 2     
  1. Variants in bold were validated by Sanger sequencing.