Table 1 Pathogenic variants

From: Pitfalls of clinical exome and gene panel testing: alternative transcripts

Variant	Gene	Panel transcript change		Alternative transcript change		AF
		Type	Details	Type	Details
a) Variants in alternative coding regions^a
chr19:13318673 delCTGCTGCTGCTGCTGCTGCTG	CACNA1A	UTR3	NM_001127221.1:c.187_167delCAGCAGCAGCAGCAGCAGCAG	Polyglutamine repeat	ENST00000614285.4_1:c.6973_6993del:p.2325_2331del	na^b
chr17:42987501 CAGCTAAC>GAT	GFAP	na	na	Frameshift	ENST00000435360.7_2:c.1292_1299ATC	0
chr17:42987511C>T	GFAP	na	na	nonsynonymous	ENST00000435360.7_2:c.G1289A:p.R430H	8e-6
chr6:39874535 delCT	MOCS1	UTR3	NM_005943.5:c.366_365delAG	Frameshift	ENST00000373195.7_1:c.1199_1200del:p.E400fs	2e-5
chr6:39902057 delCC	MOCS1	na	na	Frameshift	ENST00000373188.6_1:c.99_100del:p.G33fs	0
chr5:52404362G>A	MOCS2	na	NM_004531.4:c.-1358C>T	Stopgain	ENST00000361377.8_3:c.C130T:p.R44X	0
chr5:52404386G>A	MOCS2	na	NM_004531.4:c.-1382C>T	Stopgain	ENST00000361377.8_3:c.C106T:p.Q36X	0
chr5:52404404G>A	MOCS2	na	NM_004531.4:c.-1400C>T	Stopgain	ENST00000361377.8_3:c.C88T:p.Q30X	8e-6
chr5:52404447A>T	MOCS2	na	NM_004531.4:c.-1443T>A	Nonsynonymous	ENST00000361377.8_3:c.T45A:p.S15R	8e-6
chr5:52404459A>C	MOCS2	na	NM_004531.4:c.-1455T>G	Stopgain	ENST00000361377.8_3:c.T33G:p.Y11X	2e-5
chr5:52404473C>A	MOCS2	UTR5	NM_004531.4:c.-1469G>T	Nonsynonymous	ENST00000361377.8_3:c.G19T:p.V7F	4e-6
chr5:52405544G>A	MOCS2	UTR5	NM_004531.4:c.-2540C>T	Stopgain	ENST00000361377.8_3:c.C16T:p.Q6X	2e-5
chr5:52405545 delGCACAGCGGCACCATCCCGCCTA	MOCS2	UTR5	NM_004531.4:c.-2541_-2563 delTAGGCGGGATGGTGCCGCTGTGC	Startloss	ENST00000361377.8_3:c.-8_15del23	0
chr5:52405557C>T	MOCS2	na	NM_004531.4:c.-2553G>A	Startloss	ENST00000361377.8_3:c.G3A:p.M1I	0
chr5:52405559T>C	MOCS2	na	NM_004531.4:c.-2555A>G	Startloss	ENST00000361377.8_3:c.A1G:p.M1V	1e-5
chr9:130453077 delC	STXBP1	UTR3	NM_003165.3:c.*40delC	Frameshift	ENST00000373299.4_1:c.1726delC:p.Q576fs	0
b) Reannotated variants^a,c
chrX:18646710C>T	CDKL5	Splicing	NM_003159.2:c.2713+3C>T	Stopgain	ENST00000623535.1_2:c.C2716T:p.Q906X	0
chrX:76952065C>A	ATRX	Nonsynonymous	NM_000489.4:c.G370T:p.G124C	Stopgain	ENST00000395603.7_1:c.G370T:p.E124X	0
chr3:33106965A>T	GLB1	Nonsynonymous	NM_000404.3:c.T542A:p.I181K	Stopgain	ENST00000307377.12_1:c.T330A:p.Y110X	0
chr5:52402972G>A	MOCS2	Synonymous	NM_004531.4:c.C33T:p.F11F	Stopgain	ENST00000361377.8_3:c.C220T:p.Q74X	0

AF allele frequency in gnomAD, UTR3 3’ untranslated region, UTR5 5’ untranslated region.
^aVariant sources and data supporting pathogenicity are provided in Supplementary Table S3.
^bThe variant is located in a low complexity region that may be difficult to sequence.
^cConstraint metrics reflecting the probability of intolerance to loss-of-function variation are provided in Supplementary Table S4.

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Table 1 Pathogenic variants

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