Table 2

Genotypes of Usher type 2 and of Usher type 3 probands (novel variants in bold)

Family	USH type	Gene	Allele 1^*	Allele 2^*	Allele 1 score	Allele 2 score	Ethnicity^†
3	2	USH2A	p.Glu767SerfsX21	p.Arg4971X	P	P	Caucasian
21	2	USH2A	p.Glu767SerfsX21	p.Arg626X	P	P	Caucasian
26, 46	2	USH2A	p.Glu2288X	Unknown	P		Caucasian
29	2	USH2A	p.Arg4192His^‡	p.Arg4192His^‡	UV2	UV2	Caucasian (Italy)
32	2	USH2A	p.Glu767SerfsX21	p.His308SerfsX16	P	P	Caucasian
38	2	USH2A	p.Glu767SerfsX21	p.Arg34X	P	P	Caucasian
45	2	USH2A	p.Glu767SerfsX21	p.Ser1173X	P	P	Caucasian
53^§	2	USH2A	p.Cys1452LeufsX25	p.Cys1452LeufsX25	P	P	Indian
57	2	USH2A	p.Glu767SerfsX21	p.Cys536Arg	P	P	Caucasian
61	2	USH2A	p.Pro560LeufsX31	p.Glu2265_Tyr2266del insAsp	P	P	Caucasian
64	2	USH2A	p.Trp1607X ^¶	p.Cys620Phe	P	P	Caucasian
82	2	USH2A	c.11047+1G>A	p.Cys3575Tyr	P	UV4	Caucasian
113	2	USH2A	p.Cys982LeufsX2	p.Trp3955X^**	P	P	Arab
147	2	USH2A	p.Gln3959AsnfsX53	p.Asn4762Ser	P	UV3	Caucasian
151	2	USH2A	p.Gln1063SerfsX15	Unknown	P		Caucasian
155	2	USH2A	p.Glu767SerfsX21	p.Arg1946X	P	P	Caucasian
165	2	USH2A	p.Glu767SerfsX21	p.Trp2945X	P	P	Caucasian
171	2	USH2A	p.Glu767SerfsX21	p.Lys4816X	P	P	Caucasian
179	2	USH2A	p.Arg1504LysfsX26	p.Trp2744X	P	P	Caucasian
187	2	USH2A	p.Glu767SerfsX21	p.Gln1063SerfsX15	P	P	Caucasian
192	2	USH2A	p.Pro746Ala	c.7595-3C>G^††	UV4	P	Caucasian
193	2	USH2A	p.His308SerfsX16	c.9371+1G>C ^¶	P	P	Caucasian
194	2	USH2A	p.Thr4439Ile	p.Cys3267Arg	P	UV4	Caucasian
200	2	USH2A	p.Glu767SerfsX21	c.11390-1G>C	P	P	Caucasian
203^§	2	USH2A	p.Cys870X	p.Cys870X	P	P	Turkish Cypriot
205^§	2	USH2A	Unknown	Unknown			Indian
212, 702	2	USH2A	p.Glu767SerfsX21	p.Cys419Phe	P	P	Caucasian
215	2	USH2A	p.Glu767SerfsX21	p.Ala4153Thr ^¶	P	P	Caucasian
219, 672	2	USH2A	p.Glu767SerfsX21	p.Ala1872LeufsX58	P	P	Caucasian
220	2	USH2A	p.Arg3689X	p.Trp3521Arg	P	P	Caucasian
221	2	USH2A	Exon 47 deleted ^‡‡	Exon 47 deleted ^‡‡	P	P	Greek
225	2	USH2A	p.Asn346His	Unknown	P		Caucasian
239	2	USH2A	p.Thr4809Ile	Unknown	P		Caucasian
247	2	USH2A	p.Glu767SerfsX21	p.Gln3959AsnfsX53	P	P	Caucasian
296	2	USH2A	p.Glu767SerfsX21	p.Gln675X	P	P	Caucasian
314^§	2	USH2A	c.1841-2A>G	c.1841-2A>G	P	P	Caucasian
321	2	USH2A	p.Thr4439Ile	p.Asn346His	P	P	Caucasian
332	2	USH2A	p.Glu767SerfsX21	p.Cys620Phe	P	P	Caucasian
334, 386	2	USH2A	p.Glu4458AspfsX3	c.7595-3C>G^††	P	P	Caucasian
345	2	USH2A	p.Glu1492X	c.11047+1G>A	P	P	Caucasian
347	2	USH2A	p.Glu2288X	p.Gly268Arg	P	UV3	Unknown
355	2	USH2A	p.Glu767SerfsX21	p.Glu4458AspfsX3	P	P	Caucasian
359	2	USH2A	p.Cys5153X	p.Trp3521Arg	P	P	Caucasian
367, 17	2	USH2A	p.Glu767SerfsX21	p.Gln4541X	P	P	Caucasian
369	2	USH2A	p.Arg1504LysfsX26	p.Glu767SerfsX21	P	P	Caucasian
374	2	USH2A	p.Pro560LeufsX31	p.His340Leu	P	UV3	Caucasian
377	2	USH2A	p.Arg1777Trp	p.Asn2285Ser	UV3	UV2	Indian
385	2	USH2A	p.Glu3305ArgfsX41	p.Asn346His	P	P	Caucasian
387	2	USH2A	p.Glu767SerfsX21	p.Ile2754AsnfsX15	P	P	Caucasian
389	2	USH2A	p.Glu767SerfsX21	p.Tyr4801X	P	P	Caucasian
394	2	USH2A	p.Glu767SerfsX21	p.Glu284AspfsX38	P	P	Caucasian
398	2	USH2A	p.Gln675X	p.Gln4541X	P	P	Caucasian
401	2	USH2A	p.Glu767SerfsX21	p.Glu2288X	P	P	Caucasian
408^§	2	USH2A	p.Cys419Phe	p.Cys419Phe	P	P	Caucasian
417	2	USH2A	p.Glu767SerfsX21	p.Thr4439Ile	P	P	Caucasian
418	2	USH2A	p.Arg63X	p.Arg1549X	P	P	Caucasian
427	2	USH2A	p.Cys1452LeufsX25	Unknown	P		Afro-Caribbean
440	2	USH2A	p.Cys620Phe	Unknown	P		Caucasian
455	2	USH2A	p.Ser4377X	p.Cys419Phe	P	P	Caucasian
490	2	USH2A	p.Arg1281X	p.Met1280Ile	P	UV4	Caucasian
509	2	USH2A	p.Glu767SerfsX21	p.Trp4713X	P	P	Caucasian
545	2	USH2A	p.Glu767SerfsX21	p.Leu1378Pro	P	UV4	Caucasian
546	2	USH2A	p.Cys3281Phe	Unknown	UV2		Caucasian
549	2	USH2A	p.Gly4403ProfsX15	p.Ser1588HisfsX5	P	P	Caucasian/Philippino
558^§	2	USH2A ^‡	p.Thr281Lys	p.Thr281Lys	UV2	UV2	Turkish Cypriot
568	2	USH2A	p.Gly4403ProfsX15	Unknown	P		Caucasian
591	2	USH2A	p.Asn346His	p.Trp3521Arg	P	P	Caucasian
595	2	USH2A	p.Glu767SerfsX21	p.Trp3521Arg	P	P	Caucasian
601	2	USH2A	p.Glu767SerfsX21	p.Ser1136Asn	P	UV4	Caucasian
611	2	USH2A	p.Glu767SerfsX21	c.651+1G>A	P	P	Caucasian
620	2	USH2A	p.Glu767SerfsX21	p.Cys999LeufsX9	P	P	Caucasian
644	2	USH2A	p.Asn1967TrpfsX5	p.Arg1578Cys	P	UV4	Caucasian
648	2	USH2A	p.Arg1504LysfsX26	p.Cys419Phe	P	P	Caucasian
651	2	USH2A	p.Arg1946LeufsX22	Unknown	P		Caucasian
657	2	USH2A	p.Arg63X	Unknown	P		Caucasian
670	2	USH2A	p.Gly1751Val	p.Gly2017Cys ^§§	UV2	UV2	Indian
680	2	USH2A	p.Asn346His	p.Cys419Phe	P	P	Caucasian
683^§	2	USH2A	Exons 50–55 deleted ^‡‡	Exons 50–55 deleted ^‡‡	P	P	Kashmiri
5 fams	2	USH2A	p.Glu767SerfsX21	p.Glu767SerfsX21	P	P	Caucasian
465	2	USH2A	p.Glu767SerfsX21	c.10585G>A^§§	P	UV3	Caucasian
432	2	USH2A	p.Glu767SerfsX21	c.12295-3T>A	P	UV2	Indian
531	2	USH2A	p.Glu767SerfsX21	p.Gly257Arg	P	UV2	Unknown
669	2	USH2A	p.Glu767SerfsX21	p.Phe1868Cys	P	UV2	Unknown
9 fams	2	USH2A	p.Glu767SerfsX21	Unknown	P		Caucasian
136^§	2	GPR98	Exon 83 deleted ^¶¶	Exon 83 deleted ^¶¶	P	P	Arab Palestinian
170	2	GPR98	p.Arg2286X	p.Ser3339Asn	P	UV3	Caucasian
271	2	GPR98	p.Arg4802X	p.Ile3325Thr	P	UV2	Caucasian
275	2	GPR98	p.Asp1375His	Unknown	UV2		Caucasian
300^§	2	GPR98	p.Glu2103X	p.Gln2301X	P	P	Caucasian
357	2	GPR98	p.Arg800X	c.13433G>T ^§§	P	UV3	Caucasian
481	2	GPR98	p.Ser5048ArgfsX29	p.Val2321AlafsX4	P	P	Caucasian
665	2	GPR98	p.Ala3579ValfsX6	p.Val3363AspfsX11	P	P	Caucasian
697	2	GPR98	c.9623+1G>A	Unknown	P		Caucasian
222	2	GPR98 ^***	Unknown	Unknown			Indian
110	2	MYO7A	p.Gly1942X	Unknown	P		Caucasian
49	3	CLRN1	p.Ser50LeufsX12	p.Ser50LeufsX12	P	P	Caucasian
82	3	CLRN1	p.Asn48Lys	p.Asn48Lys	P	P	Ashkenazi Jewish

For family 29, USH2A haplotypes are not homozygous. It is possible they are p.Arg4192His hemizygous and have a deletion on the other allele.
↵* Unless stated otherwise, the alleles were not observed in control chromosomes.
↵† Caucasian: UK and European.
↵‡ Parental origin could not be determined. Patient and affected sib are homozygous for the mutation.
↵§ Consanguineous family.
↵¶ Found in 1/872 (0.11%) control chromosomes.
↵** Found in 2/860 (0.23%) control chromosomes.
↵†† Splice mutation; causes USH2A:p.Pro2533Asnfs*5.23
↵‡‡ Large deletion speculated based on patient's homozygosity of USH2A haplotypes and failure to amplify exon.
↵§§ Last nucleotide of the exon.
¶¶ Deletion strongly suspected based on homozygosity for GPR98 markers (USH2A excluded based on haplotype analysis), and apparent non-inheritance of GPR98 SNPs in the family and PCR non-amplification of patient's as well as affected sib's DNAs (supplemental figure 3).
↵*** Not reported as a consanguineous family. Usher is compatible with mutation in GPR98 (affected sibs are homozygous for a GPR98 haplotype); USH2A is excluded by haplotype analysis.
P, Pathogenic; UV unclassified variant.