Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits

Yuan, Bo; Schulze, Katharina V.; Assia Batzir, Nurit; Sinson, Jefferson; Dai, Hongzheng; Zhu, Wenmiao; Bocanegra, Francia; Fong, Chin-To; Holder, Jimmy; Nguyen, Joanne; Schaaf, Christian P.; Yang, Yaping; Bi, Weimin; Eng, Christine; Shaw, Chad; Lupski, James R.; Liu, Pengfei

doi:10.1186/s13073-022-01113-y

Table 1 Recurrent genomic deletions that are prevalent in the population

From: Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits

Region	Coordinates (GRCh38)	Population allele frequency (× 10⁻⁶)	Allele frequency in diagnostic testing (× 10⁻⁶)	Known recessive genes	Number of coding genes
2q13 NPHP1	chr2:109930242-110228182	5811	2616	NPHP1	3
15q11.2	chr15:21311962-23261294	2764	2287	-	14
16p12.1	chr16:21754781-22502804	584.0	627.8	OTOA, UQCRC2	11
16p11.2 proximal	chr16:29416551-30202090	507.6	1674	PRRT2, ALDOA, TBX6, CORO1A	35
17p12 HNPP	chr17:14170711-15567588	314.8	388.6	COX10, PMP22	9
16p13.11	chr16:14772948-16330433	311.0	433.5	NDE1, MYH11, ABCC6	15
1q21.1 BP3-BP4	chr1:146380249-148811725	268.2	672.6	-	15
13q12.12	chr13:22911590-24323812	201.8	104.6	SGCG, SACS, MIPEP	7
1q21 TAR	chr1:144904297-146209950	178.0	269.0	PEX11B, RBM8A, POLR3GL, HJV	22
22q11.2 LCRA-D	chr22:18530098-21214537	141.7	4499	PRODH, SLC25A1, CDC45, GP1BB, TXNRD2, TANGO2, SCARF2, PI4KA, SNAP29, LZTR1	48
10q11.21q11.23	chr10:45765081-49954967	135.3	74.73	RBP3, ERCC6, SLC18A3, CHAT	38
16p11.2 distal	chr16:28706949-29049993	137.7	254.1	TUFM, ATP2A1, CD19, LAT	11
2q13	chr2:110494056-112385043	125.8	149.5	ANAPC1, MERTK	11
7q11.23	chr7:73089294-74862006	120.0	1375	NCF1	28
2q21.1	chr2:130623447-131386379	97.33	119.6	-	9
15q13.3 BP4-BP5	chr15:30246847-32496522	99.70	896.8	FAN1, TRPM1, OTUD7A	13
2q11.2	chr2:95759114-97430329	73.60	74.73	ADRA2B, NCAPH, LMAN2L, CNNM4	24
17q12	chr17:36300613-38034442	68.86	463.4	ZNHIT3, PIGW	21
17p11.2 Smith Magenis Syndrome	chr17:16777950-20450859	53.33	687.6	TNFRSF13B, ATPAF2, MYO15A, MEIF2, TOP3A, GRAP, B9D1, ALDH3A2	48
15q11q13 BP3-BP4	chr15:28580349-30417865	37.98	134.5	NSMCE3	10
3q29	chr3:195963652-197626678	21.36	194.3	TFRC, PCYT1A, TCTEX1D2, RNF168, NRROS, CEP19	23
17q11.2	chr17:30621877-32037969	21.36	149.5	-	14
15q11 Prader-Willi/ Angelman syndromes BP1-BP3	chr15:21976318-28537425	19.89	687.6	OCA2, HERC2	27
15q11 Prader-Willi/ Angelman syndromes BP2-BP3	chr15:23247414-28447477	19.89	657.7	OCA2, HERC2	17
22q11.2 LCRD-H	chr22:21206521-24255497	11.87	59.79	IGLL1	45
8p23.1	chr8:7596999-12344083	9.495	134.5	RP1L1, FDFT1	50
10q23	chr10:79733715-87254783	7.121	59.79	MAT1A, CDHR1	31
15q24 BPA-BPC	chr15:72628218-75278711	2.374	74.73	BBS4, STRA6, EDC3, MPI, COX5A	40
15q11q13 BP3-BP5	chr15:28569118-32447357	2.374	59.79	NSMCE3, FAN1, TRPM1, OTUD7A	21
7q11.23 distal	chr7:75456184-76629927	2.374	29.89	POR, MDH2	19

Regions are listed in descending order by population prevalence. Genes in the “Known recessive gene” column are ordered by coordinate map positions. Even though it is the third highest NAHR-mediated deletions, the Xp22.31-STS deletion is not included in this table because the current list focuses on autosomal recessive conditions. The gene OTUD7A in 15q13.3 BP4-BP5 is not reported to cause a recessive disease at the time of this study; however, patient analysis results from this study support this gene as a candidate recessive disease gene

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