Table 1.

Molecular Genetic Testing Used in Usher Syndrome Type I (USH1)

Gene 1USH1 SubtypeProportion of USH1
Attributed to Pathogenic
Variants 2 in Gene 3
Proportion of Pathogenic Variants 2
Detected by Method
Sequence analysis 4Gene-targeted deletion/
duplication analysis 5
MYO7A USH1B53%-70%~98% 6<2% 7
USH1C USH1C6%-15% 8>98%2 reported 9, 10
CDH23 USH1D10%-20%~85% 11<15% 12
PCDH15 USH1F7%-12% 13~75%~25% 14, 15
USH1G USH1GRare (0%-4%)>85%2 reported 15
CIB2 USH1JUnknown1 reported 16None reported 16
Unknown 1710%-15% 18NA
1.
2.

See Molecular Genetics for information on variants detected in this gene.

3.
4.

Sequence analysis detects variants that are benign, likely benign, of uncertain significance, likely pathogenic, or pathogenic. Variants may include small intragenic deletions/insertions and missense, nonsense, and splice-site variants; typically, exon or whole-gene deletions/duplications are not detected. For issues to consider in interpretation of sequence analysis results, click here.

5.

Gene-targeted deletion/duplication analysis detects intragenic deletions or duplications. Methods used may include a range of techniques such as quantitative PCR, long-range PCR multiplex, ligation-dependent probe amplification (MLPA), and a gene-targeted microarray designed to detect single-exon deletions or duplications.

6.
7.

The majority of reported pathogenic variants are detectable by sequence analysis; however, intragenic multiexon deletions have been reported [Adato et al 1997, Baux et al 2008, Roux et al 2011, Bonnet et al 2016].

8.

Almost all Usher syndrome type I in the Acadian population is caused by USH1C pathogenic variants. Five pathogenic variants in USH1C have been identified in 53 Acadian individuals with USH1 from Louisiana and Canada [Lentz et al, ongoing Natural History Study, unpublished]. Of these, c.216G>A is the most common variant (95/106 alleles, 90%), followed by c.238dupC (6/106 alleles, 6%).

9.
10.

Homozygous 11p15-p14 deletion syndrome (see Genetically Related Disorders) is caused by a contiguous gene deletion that includes USH1C and ABCC8 and has been observed in families from Saudi Arabia and Kuwait [Bitner-Glindzicz et al 2000, Al Mutair et al 2013].

11.
12.

The majority of reported pathogenic variants are detectable by sequence analysis; however, intragenic deletions and duplications have been reported [Nakanishi et al 2010, Roux et al 2011, Aparisi et al 2014, Bonnet et al 2016].

13.

p.Arg245Ter (c.733C>T) is detected in a large percentage of Ashkenazi Jewish individuals with PCDH15-Usher syndrome type I.

14.
15.
16.

Riazuddin et al [2012]. Note: Booth et al [2018] suggest that CIB2 pathogenic variants cause DFNB48 and not USH1J.

17.

USH1E has been mapped to 21q21; USH1H has been mapped to 15q22-q23 [Ahmed et al 2009]; USH1K has been mapped to 10p11.21-q21.1 [Jaworek et al 2012].

18.

From: Usher Syndrome Type I

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