Copy number variants encompassing Mendelian disease genes in a large multigenerational family segregating bipolar disorder

Kember, Rachel L; Georgi, Benjamin; Bailey-Wilson, Joan E; Stambolian, Dwight; Paul, Steven M; Bućan, Maja

doi:10.1186/s12863-015-0184-1

Table 3 CNVs within genes

From: Copy number variants encompassing Mendelian disease genes in a large multigenerational family segregating bipolar disorder

Cytoband	Start	Stop	No. snp	length (bp)	CN	Contained genes	Frequency	No. subjects	No. affected	No. families	Predicted effect	FBAT	EMMAX	Previous disease associations for gene
1p36.21	13171723	13218942	31	47220	0&1	LOC440563	Rare	38	13	15	Gene del	1	0.1887
1q22	155152205	155162067	22	13287	3	*MUC1, TRIM46*	Amish specific	28	13	32	Partial gene dup	0.0711	0.1535	Kidney disease [42]
1q24.1	165644865	165649715	9	4851	1	ALDH9A1	Very rare	17	7	12	Exonic del	1	0.1434
2q31.1	176929113	177000696	86	71584	3	EVX2, *HOXD10, HOXD11, HOXD12, HOXD13, HOXD8, HOXD9*	Amish specific	45	15	32	Gene dup	0.4122	0.9834	Limb and genital abnormalities [43,44]
2q37.3	241500674	241516094	20	24920	3	DUSP28, RNPEPL1	Very rare	74	13	43	Partial gene dup	0.4226	0.3229
2q37.3	241482099	241516094	20	24920	3	ANKMY1, DUSP28, RNPEPL1	Very rare	31	7	23	Partial gene dup for ANKMY1 and RNPEPL1, gene dup for DUSP28	0.0007	0.3229
3p21.2	51989546	51995419	11	10143	3	GPR62, PCBP4	Amish specific	72	17	47	Partial gene dup	0.0412	0.0238
3p25.3	11411823	11414339	5	2517	0&1	*ATG7*	Rare	46	13	24	Intronic del	0.7557	0.7020	Frontotemporal dementia, Parkinsons disease [45]
3q29	193136358	193140348	9	3991	0&1	*ATP13A4*	Rare	41	9	18	Intronic del	0.7389	0.2519	Autism [46]
4q22.1	91907363	91913329	16	10710	1	FAM190A	Amish Specific	34	6	21	Intronic del	0.0099	0.0794
5q35.3	179221537	179238794	25	32170	3	*LTC4S, MGAT4B, MIR1229, SQSTM1, MAML1*	Amish specific	79	17	36	Partial gene dup for LTC4S and SQSTM1, gene dup for MGAT4B and MIR1229	0.6641	0.0973	Venous thromboembolism and ischaemic stroke [47], Paget disease of bone [48]
5q35.3	179211629	179231681	25	32170	3	*LTC4S, MGAT4B, MIR1229*	Amish specific	61	14	36	Gene dup	0.2513	0.0973	Venous thromboembolism and ischaemic stroke [47]
6p21.32	32610719	32614917	10	4199	1	HLA-DQA1	Rare	25	7	13	Exonic del	1	0.0574
6p25.3	1612234	1620037	15	9536	3	*FOXC1*	Very rare	47	14	23	Exonic dup	1	0.5815	Axenfeld-Rieger anomaly [49]
6q26	163041460	163139315	64	99376	1	*PARK2*	Very rare	21	5	11	Exonic del	0.5637	0.5534	Parkinsons disease [50], Autism [51]
7q22.1	100968058	101063059	159	183210	3	EMID2	Rare	100	25	38	Exonic dup	0.0330	0.7031
7q36.1	149461487	149516968	67	55482	3	SSPO, ZNF467	Amish specific	154	39	68	Partial gene dup	0.8907	0.1100
8p21.3	21943602	22024523	80	62524	3	FAM160B2, HR, NUDT18	Amish specific	112	20	59	Partial gene dup for FAM160B2 and HR, gene dup for NUDT18	0.0284	0.9422	Alopecia universalis [52], Congenital Atrichia [53]
8p22	15947559	16023673	118	76115	1	*MSR1*	Rare	19	3	7	Partial gene del	0.0833	0.6317	Prostate cancer [54]
8p22	15419777	15432653	24	21108	1	*TUSC3*	Very rare	19	3	7	Intronic del	0.0833	0.6317	Intellectual disability [55]
9q34.11	130497180	130518716	22	29513	3	SH2D3C, TOR2A	Amish specific	59	7	33	Partial gene dup for TOR2A, gene dup for SH2D3C	0.0116	0.4779
10q11.21	45222200	45359483	125	151274	3	TMEM72-AS1	Rare	38	11	15	Partial gene dup	0.4386	0.5237
10q21.3	68239474	68422442	209	182969	1	*CTNNA3*	Very rare	19	5	10	Partial gene del	0.6547	0.5957	Arrhythmogenic right ventricular cardiomyopathy [56]
11p11.2	45916436	45931646	24	29093	3	C11orf94, *MAPK8IP1, PEX16*	Amish specific	46	8	28	Partial gene dup for MAPK8IP1 and PEX16, gene dup for C11orf94	0.0197	0.0402	Diabetes type 2 [57], Zellweger syndrome [58]
11p15.4	8959020	8964938	11	5919	1	ASCL3	Very rare	28	6	12	Gene del	0.4795	0.3681
13q34	112712459	112726336	26	26199	3	SOX1	Amish specific	109	23	53	Gene dup	0.0254	0.0749	Neuronal development [59]
13q34	114518789	114530659	31	17552	3	GAS6	Very rare	92	21	45	Partial gene dup	0.6946	0.6193
14q23.2	63957653	63962909	10	6398	1	PPP2R5E	Very rare	23	5	12	Intronic del	0.2568	0.1877
15q11.2	24345146	24496990	76	152110	1	PWRN2	Rare	48	20	15	Gene del	0.1967	0.4189	Prader-Willi region [60]
15q26.1	90615898	90636762	28	26809	3	*IDH2, ZNF710*	Amish specific	27	8	13	Partial gene dup	0.7389	0.3569	D-2-hydroxyglutaric aciduria, type II [61]
16p12.1	27337036	27350687	15	20228	0&1	IL4R	Very rare	31	9	15	Exonic del	0.7812	0.1062
17p13.3	811982	1183612	665	456481	3	ABR, BHLHA9, MIR3183, NXN, TIMM22, TUSC5	Very rare	23	3	12	Partial gene dup for NXN and TUSC5, gene dup for ABR, BHLHA9, MIR3183 and TIMM22	0.6547	0.3319
18q23	77150335	77162816	40	24952	3	*NFATC1*	Amish specific	41	13	23	Exonic dup	0.8273	0.1415	Tricuspid atresia [62]
18q23	76725624	76767375	35	41752	3	SALL3	Very rare	37	11	30	Gene dup	0.1336	0.0864
18q23	77241092	77251061	21	16450	3	NFATC1	Amish specific	31	13	19	Exonic dup	0.3938	0.1313
21q22.3	44822871	44868895	35	46025	3	SIK1	Rare	95	22	38	Gene dup	0.2800	0.5553

CNVs shown are rare in controls (present in fewer than 5% of controls. Rare: <5%, Very rare: <1%, Amish Specific: not found in controls), and common in the Amish (present in more than 5% of individuals). Contained genes shows all genes in CNV, disease genes are highlighted in bold. FBAT and EMMAX p-values for association analysis for Bipolar disorder are included, p<0.05 are in bold.

Back to article page

ISSN: 2730-6844

Contact us

General enquiries: journalsubmissions@springernature.com

BMC Genomic Data

Contact us