Genetics in Keratoconus: where are we?

Bykhovskaya, Yelena; Margines, Benjamin; Rabinowitz, Yaron S.

doi:10.1186/s40662-016-0047-5

Eye and Vision

Table 1 KC genes and identified variants

From: Genetics in Keratoconus: where are we?

Gene	Function	CHR	Variant (s)	Method (Reference)	Variant Location	Ref
LOX	Lysyl oxidase, participates in collagen cross-linking	5q23.2	rs10519694	GWLS/LD/FM	Intron	[25]
			rs1800449/rs2288393	GWLS/LD/FM	Missense	[25, 29]
			rs1800449/rs2288393	TG	Missense	[25, 29]
			rs41407546	S	Missense	UN
			rs2956540	GWLS/LD/FM	Intron	[25, 29–31]
			rs2956540	TG	Intron	[25, 29–31]
COL5A1	Collagen type V, alpha-1 chain, part of fibril-forming corneal collagen	9q34.2-q34.3	rs1536482	GWLS/FM/CCT GWAS	5′ near gene	[74, 111]
COL5A1		9q34.2-q34.3	rs7044529	GWLS/FM/CCT GWAS	Intron	[74, 108, 111]
CAST	Calpain/calpastatin, proteolytic degradation	5q15	rs4434401	GWLS/FM	Intron	[37]
RAB3GAP1	Rab GTPase activating protein, regulates exocytosis	2q21.3	rs4954218	GWAS	5′ near gene	[56, 60]
HGF	Hepatocyte growth factor, involved in corneal wound healing	7q21.1	rs3735520	GWAS, TG	1 KB promoter	[29, 54]
			rs1014091	GWAS, S	1 KB promoter	[54, 55]
			rs17501108	S	1 KB promoter	[55]
			rs2286194	S	intron	[55]
FNDC3B	Fibronectin, extracellular matrix protein	3q26.31	rs4894535	CCT GWAS	Intron	[74]
FOXO1	Transcription factor	13q14.1	rs2721051	CCT GWAS, LA CCT GWAS	3′ near gene	[74, 108]
TGFBI	Transforming growth factor beta induced	5q31.1	Multiple rare variants	S	Exon	[66, 67]
ZNF469	Transcription factor, regulates corneal collagen structure and synthesis	16q24.2	rs9938149	CCT GWAS, TG	3′ near gene	[74, 112]
ZNF469		16q24.2	Multiple rare variants	S	Exon	[62–64]
DOCK9	Dedicator of cytokinesis 9, Guanine nucleotide-exchange factor	13q32.3	c.2262A > C p.Gln754His	GWLS/S	Missense	[41]
MPDZ-NF1B	Not available	9p23	rs1324183	CCT GWAS, TG	Intergenic	[30, 74, 112]
WNT10A	Member of WNT gene family of secreted signaling proteins	2q35	rs121908120	CCT GWAS	Missense	[113]
ZEB1	Zinc finger transcription factor	10p11.22	c.1920G > T; p.Gln640His	S	Missense	[84, 85]
SOD1	Superoxide dismutase 1, cytoplasmic antioxidant enzyme	21q22.11	Multiple SNVs, deletion	S	Intron	[99, 115]
IL1A	Interleukin 1alpha, cytokine	2q13	rs2071376	TG, S	Intron	[91, 119]
IL1B	Interleukin 1beta, cytokine	2q13	rs1143627	TG, S	Promoter	[119–121]
IL1B	Interleukin 1beta, cytokine	2q13	rs16944	TG, S	Promoter	[119–121]
COL4A3	Collagen type IV, alpha-3 chain, structural part of corneal membranes	2q36.3	Multiple SNVs	S	Missense	[123]
COL4A4	Collagen type IV, alpha-4 chain, structural part of corneal membranes	2q36.3	Multiple SNVs	S	Missense	[123, 124]
VSX1	Visual system homeobox 1, transcription factor	20p11.2	Multiple SNVs	S	Missense, silent, intronic	[133]

Table abbreviations: KC = keratoconus; CHR = chromosome; GWLS = genome-wide linkage study; GWAS = genome-wide association study; LD = linkage disequilibrium; FM = fine mapping; S = sequencing; TG = targeted genotyping; CCT = central corneal thickness; SNV = single nucleotide variant; LA = Latino; UN = unpublished data

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ISSN: 2326-0254

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