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

Ma, Man Chun John; Atanur, Santosh S; Aitman, Timothy J; Kwitek, Anne E

doi:10.1186/1471-2164-15-197

BMC Genomics

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
RGD1563300	42,228,845	42,229,431	Similar to 60S ribosomal protein L29 (P23)	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
Prl5a2	42,984,939	42,991,275	Prolactin family 5, subfamily a, member 2	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	Benign
				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
Amph	53,558,804	53,802,936	Amphiphysin	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

Variants in bold were validated by Sanger sequencing.

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ISSN: 1471-2164

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