TABLE 4.

Reclassification of previously analyzed cases

					Variant summary
Patient index	Pub. status	Reclassified status	Reason	OMIM disease phenotype	Gene	Genomic	cDNA	Protein
ATX12	VUS	N	Variants too common in population	270700	ZFYVE26	14:68236320C>T 14:68265135G>A	c.5612G>A c.1844C>T	p.Cys1871Tyr p.Ser615Phe
	N	Path	Known pathogenic variant, consistent phenotype	617046	FARS2	6:5369210C>A Conifer: 6:5109590–5613554del XHMM: 6:5404729–5431977del	c.407C>A c.(613_46)del	p.Pro136His p.?
ATX15a	N	Path	Known pathogenic variant, consistent phenotype, segregates with disease in family	545000	MT-TK	m.8344A>G	-	-
ATX19	N	VUS	Rare variant, consistent phenotype	617931	PUM1	1:31532131C>T	c.283G>A	p.Gly95Arg
ATX23a	N	Path	Rare variants, consistent phenotype, segregates with disease in family	616907	CAPN1	11:64953668_64953669delAG 11:64974125_64974129delAGAGA	c.618_619delAG c.1545_1549delAGAGA	p.Gly208Glnfs*7 p.Lys517Cysfs*8
ATX27	VUS	N	Variant too common in population	600224	SPTBN2	11:66472288G>A	c.2459C>T	p.Thr820Met
ATX31	N	VUS	Rare variants, consistent phenotype	610743	SYNE1	6:152470724C>T 6:152737976C>T	c.24317G>A c.5617G>A	p.Ser8106Asn p.Ala1873Thr
ATX36	VUS	N	Variant does not segregate with disease in family	222300	WFS1	4:6302816C>G	c.1294C>G	p.Leu432Val
ATX38	VUS	Pathb	Known pathogenic variant, consistent phenotypeb	604360	SPG11	15:44876420delCT	c.5456_5457delAG	p.Glu1819Alafs*10
ATX39	VUS	LP	Known pathogenic variant, consistent phenotype	614436	LRSAM1	9:130265074T>C	c.2068T>C	p.Cys690Arg
ATX40	N	VUS	Rare variant, consistent phenotype	615889	AARS2	6:44269870C>T	c.2525G>A	p.Arg842Gln
ATX42	N	VUS	Rare variant, consistent phenotype	607259	SPG7	16:89598384G>A	c.1060G>A	p.Gly354Arg
ATX45	N	VUS	Rare variant, consistent phenotype	615889	AARS2	chr6:44269119_44269120delGA	c.2680_2681delTC	p.Val895Alafs*10
ATX50	N	VUS	Rare variant, consistent phenotype	213600	SLC20A2	8:42297115C>A	c.787G>T	p.Val263Phe
ATX52	VUS N	N VUS	Variant is too common in population Rare variant, consistent phenotype	612020 616439	PNPLA6 TBK1	19:7607741C>T 12:64879243C>T	c.1340C>T c.1198C>T	p.Pro447Leu p.Pro400Ser
ATX64	VUS	N	Variant is too common in population	614251	EIF4G1	3:184039843A>T	c.1492A>T	p.Ile498Phe
ATX66	VUS	N	Variants too common in population	263570	GBE1	3:81640290A>C 3:81810551G>T	c.1134T>G c.118C>A	p.Ser378Arg p.Pro40Thr
ATX68	VUS	N	Variants do not segregate with disease in family	614895 271245	PRX TWNK	19:40900066G>T 10:102749087C>T	c.4193C>A c.1120C>T	p.Ala1398Asp p.Arg374Trp
ATX74	VUS	N	Variant is too common in population, does not segregate with disease in family	613908	TGM6	20:2375121T>G	c.31T>G	p.Trp11Gly

Note: A Total of 76 cases from Fogel et al. (2014) were reanalyzed using current methods (see text). Population frequency determined by use of the ExAC (http://exac.broadinstitute.org/) and gnomAD (https://gnomad.broadinstitute.org/) databases.

Abbreviations: cDNA, complementary DNA; LP, likely pathogenic; N, nondiagnostic; OMIM, Online Mendelian Inheritance in Man; Path, pathogenic; VUS, variant of uncertain clinical significance.

^aThese patients were originally reported with sporadic disorders but subsequently reclassified as familial when additional family members were clinically evaluated.

^bThis recessive disorder was diagnosed clinically due to its distinctive phenotype, a second pathogenic variant is presumed to be noncoding.