Identification and functional characterization of two novel mutations in KCNJ10 and PI4KB in SeSAME syndrome without electrolyte imbalance

Nadella, Ravi K.; Chellappa, Anirudh; Subramaniam, Anand G.; More, Ravi Prabhakar; Shetty, Srividya; Prakash, Suriya; Ratna, Nikhil; Vandana, V. P.; Purushottam, Meera; Saini, Jitender; Viswanath, Biju; Bindu, P. S.; Nagappa, Madhu; Mehta, Bhupesh; Jain, Sanjeev; Kannan, Ramakrishnan

doi:10.1186/s40246-019-0236-0

Human Genomics

Table 2 Exonic SNPs identified by both ROH and non-ROH analysis pipeline

From: Identification and functional characterization of two novel mutations in KCNJ10 and PI4KB in SeSAME syndrome without electrolyte imbalance

Gene and description	Cellular function^a	Chromosome location	MAF (<= 0.01) in 1 kg_all ; ExAC_all	rsID (dbSNP)	Pathogenicity scale^b (Suhas et.al 2018)	Tissue expression^a	Gene-Disease Association
Exome SNPs assessed by allele frequencies in AR inheritance pattern (non-ROH method)
KCNJ10 (inwardly rectifying potassium channel)	K⁺ homeostasis	c.A868G:p.T290A	Novel	NA	6/6	Brain, kidney	SeSAME syndrome; (Scholl et al., 2009)
PI4KB (phosphatidylinositol 4-kinase beta)	Phosphatidylinositol signaling	c.A215G:p.K72R	Novel	NA	2/6	Brain, liver	NA
PVRL4 (Nectin 4)	Cell Adhesion signaling	c:C320T:p.P107L	0.004; 0.0052	rs78105657	3/6	Pancreas, skin	Ectodermal dysplasia- Syndactyly syndrome 1; (Ahmad et al. 2018)
RORC (RAR-related orphan receptor C)	Nuclear signaling	c.G686A:p.S229N	0.002; 0.0035	rs41263732	NP	Kidney, colon	Primary immunodeficiency-43 (Okada et al., 2015)
FCRL1 (Fc receptor-like 1)	Immune signaling	c:C1035G:p.S345R	0.003; 0.003	rs149687405	NP	Blood, tonsil	NA
FLG2 (Filaggrin-2)	Calcium signaling	c.A6260G:p.H2087R	0.004; 0.0068	rs141384852	NP	Skin, liver	NA
NIT1(Nitrilase 1)	Apoptosis	c.A4G:p.T2A	0.0009; 0.0051	rs138523655	2/6	Brain, liver	NA
Exome SNPs assessed by runs of homozygosity (ROH method)
KCNJ10 (inwardly rectifying potassium channel)	K⁺ homeostasis	c.A868G:p.T290A	Novel	NA	6/6	Brain, kidney	SeSAME syndrome; (Scholl et al. 2009)
HSPA6 (heat shock protein Family A, HSP70)	Molecular chaperone in protein homeostasis	c.C592T:p.L198F	0.124201;0.1165	rs1079109	3/6	Brain, muscles, kidney	Sensory disturbances; (Kobayashi et al. 2013)

NP non-pathogenic
^aAccording to GeneCards Database (http://www.genercards.org)
^bIn addition to the two prediction algorithms SIFT and PolyPhen mentioned in Fig. 2, we used four more prediction algorithms (LRT_pred, MutationTaster_pred, MutationAssessor_pred and FATHMM_pred)

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