USH2A SNPs

USH2A

Usherin (USH2A), a 71-exon coding gene located on human chromosome 1q41], encodes a 5202 residue multi-domain protein comprised of a signal peptide, a PDZ1 binding domain (for USH1C and WHRN), 1 laminin NT-terminal domain, 10 laminin EGF-like domains, 4 fibronectin type-III domains (for collagen IV and fibronectin), and 2 laminin G-like domains followed by 31 additional fibronectin type-III domains all tethered to the cytoplasmic exterior by a single transmembrane domain.

The usherin gene is expressed in the basement membrane of many (but not all) cell types, notably in ear interstereocilia ankles and below retinal pigment epithelial cells (Bruch's layer). When normal function is disrupted by mutations in both copies, non-vestibular sensorineural deafness and degeneration of retinal photoreceptor cells called Usher syndrome type IIA results.

Initially, only the first 21 exons were studied but later it emerged that the gene was much longer and mutations along the entire length of the protein all led to the same disease: 125, 163, 230, 268, 303, 334, 346, 352, 478, 536, 595, 644, 713, 759, 1212, 1349, 1486, 1572, 1665, 1757, 2080, 2086, 2106, 2169, 2238, 2265, 2266, 2292, 2562, 2875, 2886, 3088, 3099, 3115, 3124, 3144, 3199, 3411, 3504, 3521, 3590, 3835, 3868, 3893, 4054, 4115, 4232, 4433, 4439, 4487, 4592, 4624, 4795, 5031.

This note evaluates a tentative new SNP in USH2A with comparative genomics. The mutation occurs as a non-hotspot G-->A transition causing a seemingly innoculous S-->N amino acid change at postion 3743. This is just downstream from a glycosylation motif and very near known FN3 interdomain contact residues and a cytokine receptor motif (according to its annotation at SwissProt). This residue lies in the 22nd fibronectin domain which is split across exon 56 and 57.

This change will be shown significant (not plausibly neutral). It could represent an adaptive innovation but is more likely deleterious. The gene is single-copy so there are no prospects for compensation by a second gene. Consequently the mutation, if present on both alleles, could well result in a new form of Usher syndrome type IIA.

Background

Fibronectin FN3 domains are an ancient and exceedingly common domain in bilaterans with 2% of the human proteome containing them (400 genes), often in multiple tandem copies having a role in cell adhesion. However they are not particularly well conserved in primary sequence, though the tertiary structure likely holds up well enough for the structure at 3743 to be determined with both serine and asparagine present.

Here the best blastp match within the human proteome to the FN3 domain containg residue 3743 is to a fibronectin domain of PTPRQ, a dimly related protein tyrosine phosphatase with merely 28% of the fibronectin domains. The best match internally to the other 30 FN3 domains of USH2A is not noticably better, suggesting very substantial divergence since these domains duplicated from a common source.

As can be seen below, the internal fibronectin repeats are most often T at the position corresponding to S3743 though other residues, not including the asparagine of S3743N, also occur. Here the numbering of better matches within the full length protein indicates they do not always correspond in quality to the linear ordering of the FN3 repeat within the protein.

FBN22 1     WSLPEKPNGLVSQYQLSRNGNLLFLGGSEEQNFTDKNLEPNS
            WSLPEKPNGLVSQYQLSRNGNLLFLGGSEEQNFTDKNLEPNS
FBN.. 3702  WSLPEKPNGLVSQYQLSRNGNLLFLGGSEEQNFTDKNLEPNS

FBN22 1     WSLPEKPNGLVSQYQLSRNGN-LLFLGGSEEQNFTDKNLEPNS
            WS+PEK NG++ +YQ+ + G  L+    ++ +  T   L+P +
FBN.. 3610  WSVPEKSNGVIKEYQIRQVGKGLIHTDTTDRRQHTVTGLQPYT

FBN22 1     WSLPEKPNGLVSQYQLSRNGNLL-FLGGSEEQNFTDKNLEPNS
            W  PE+ NG++  Y+L RN  L  F       N+TD+ L P S
FBN.. 4285  WIPPEQSNGIIQSYRLQRNEMLYPFSFDPVTFNYTDEELLPFS

FBN22 1     WSLPEKPNGLVSQYQLSRNGNLLFLGGSEEQNFTDKNLEPNS
            W  P K NG+++ Y +  +G L         N T  +L P + 
FBN.. 2553  WQHPRKSNGVITHYNIYLHGRLYLRTPGNVTNCTVMHLHPYT

FBN22 1     WSLPEKPNGLVSQYQLSRNGNLLFLGGSEEQNFTDKNLEPNS
            W  P  PNG +  Y+L R+G +++ G   E  + D  L P  
FBN.. 4464  WKPPRNPNGQIRSYELRRDGTIVYTG--LETRYRDFTLTPGV

FBN22 1     WSLPEKPNGLVSQYQLSRNGNLLFLGGSEEQNFTDKNLEPNS
            W+ P+K NG+++QY L  +G L++ G   E+N+T  +L   + 
FBN.. 2075  WNPPKKANGIITQYCLYMDGRLIYSG--SEENYTVTDLAVFT

FBN22 1     WSLPEKPNGLVSQYQLSRNGNLLFLGGSEEQNFTDKN-LEPNS
            W  P + NG +  Y L RNG   F G S   +F+DK  ++P   
FBN.. 3521  WRKPIQSNGPIIYYILLRNGIERFRGTS--LSFSDKEGIQPFQ

FBN22 1     WSLPEKPNGLVSQYQLSRNGNLLFLGGSEEQNFTDKNLEPNS
            W+ P  PNG+V++Y +  N  L   G +   +F  ++L P +
FBN.. 3040  WTSPSNPNGVVTEYSIYVNNKLYKTGMNVPGSFILRDLSPFT

FBN22 1     WSLPEKPNGLVSQYQLSRN-------GNLLFLGGSEEQNFTDKN--LEPNS
            W  P  PNGLV  + + R          L+ L  S    F DK   L P +
FBN.. 2644  WQPPTHPNGLVENFTIERRVKGKEEVTTLVTLPRSHSMRFIDKTSALSPWT

FBN22 1     WSLPEKPNGLVSQYQLSRNGNLLFLGGSEEQNFTDKNLEPNS
            WS P + NG++  Y +  +G L + G + +  F  + L+P + 
FBN.. 4087  WSEPMRTNGVIKTYNIFSDGFLEYSGLNRQ--FLFRRLDPFT

FBN22 1     WSLPEKPNGLVSQYQLSRNGNLLFLGGSEE----QNFTDKNLEPNS
            WS P+ PN     Y L R+G  ++    +     Q F D +L P +
FBN.. 1074  WSPPDSPNAHWLTYSLLRDGFEIYTTEDQYPYSIQYFLDTDLLPYT

FBN22 1     WSLPEKPNGLVSQYQLSRNG------NLLFLGGSEEQNFTDK--NLEPNS
            W  PEKPNG++  Y + R        ++LF+       F D+   L P + 
FBN.. 3887  WMPPEKPNGIIINYFIYRRPAGIEEESVLFVWSEGALEFMDEGDTLRPFT

FBN22 1     WSLPEKPNGLVSQYQLSRNGNLLFLGGSEEQNFTDKNLEPNS
            WS P   NG +++Y L R  N   L G +       +L+P S
FBN.. 4376  WSPPTVQNGKITKY-LVRYDNKESLAG-QGLCLLVSHLQPYS

FBN22 1     WSLPEKPNGLVSQYQL--------SRNGNLLFLGGSEEQNFTDKNLEPNS
            W+ P +PNG V  Y+L         R  N + +      +F D  L P + 
FBN.. 4657  WTGPLQPNGKVLYYELYRRQIATQPRKSNPVLIYNGSSTSFIDSELLPFT

FBN22 1     WSLPEKPNGLVSQYQL------SRNGNLLFLGGSEE----QNFTDKNLEPNS
            W  P + NG +  Y L       R   ++ +  +      Q++    L+P  
FBN.. 4552  WDPPVRTNGDIINYTLFIRELFERETKIIHINTTHNSFGMQSYIVNQLKPFH

FBN22 1     WSLPEKPNGLVSQYQLSRN-------GN--------LLFLGGSEEQN---FTDKNLEPNS  42
            WS P  PNG + +Y++ R        GN        ++F   + E+N   + D  L+P +
FBN.. 4175  WSEPVNPNGKIIRYEVIRRCFEGKAWGNQTIQADEKIVFTEYNTERNTFMYNDTGLQPWT  4234

Pseudogene issues

Long isoform USH2A transcripts are over 15,000 bp in length. Consequently position 3743 is not even represented in the set of all human direct transcripts. Even should a retrogene arise from retropositioing, it is unlikely that the process would extent upstream so many exons. Unsurprisingly no processed pseudogenes are evident in any mammalian genome (tblastn of wgs division of GenBank). Thus no potential for confusion exists in locating orthologs of USH2A even in distant species with incomplete genomes.

Paralog issues

No close paralog exists in the human proteome according to the UCSC GeneSorter track. The nearest matches are to other proteins containing laminin or fibronectin domains. No potential for confusion with other genes exists within vertebrates; however comparative genomics at and before teleost fish divergence needs more careful treatment because of whole genome and domain expansion.

Tandem domain repeat issues

In proteins with multiple copies of a given domain, both expansion and contraction can occur over evolutionary timescales resulting in different numbers of repeats in different clades. Under these circumstances it can be difficult to establish orthologs of a given domain. However here the fibronectin domains diverged early on and the 22nd domain seems to be present in all vertebrates with genome projects as a single-copy domain (meaning here no recent duplications or losses).

Known variations

There are no known issues with alternative splicing that would affect the fibronectin domain under consideration here. As noted earlier, a short version of the protein studied initially does not contain residue 3743 at all.

Comparative genomics

USH2A_homSap 
USH2A_panTro 
USH2A_gorGor 
USH2A_ponAbe 
USH2A_rheMac 
USH2A_calJac 
USH2A_micMur 
USH2A_otoGar 
USH2A_tupBel 
USH2A_musMus 
USH2A_ratNor 
USH2A_criGri 
USH2A_dipOrd 
USH2A_cavPor 
USH2A_speTri 
USH2A_oryCun 
USH2A_ochPri 
USH2A_vicPac 
USH2A_susScr 
USH2A_turTru 
USH2A_bosTau 
USH2A_equCab 
USH2A_felCat 
USH2A_canFam 
USH2A_myoLuc 
USH2A_eriEur 
USH2A_sorAra 
USH2A_loxAfr 
USH2A_proCap 
USH2A_echTel 
USH2A_monDom 
USH2A_macEug 
USH2A_sarHar1 
USH2A_ornAna 
USH2A_galGal 
USH2A_taeGut 
USH2A_anoCar 
USH2A_xenTro 
USH2A_tetNig 
USH2A_takRub 
USH2A_gasAcu 
USH2A_oryLat 
USH2A_danRer 
USH2A_oncMyk 
USH2A_pimPro 
USH2A_calMil 
USH2A_petMar 
USH2A_braFlo 
USH2A_strPur 
USH2A_helRob
USH2A_nemVec