Rather than being random events, many rearrangements characterised by non‐allelic homologous recombination reflect genome architecture.11
Abundant repeat elements, for example, lead to large deletions of MECP2
in approximately 25% of cases of classic Rett syndrome. These deletions are facilitated by a region in intron 2 that is highly enriched for Alu repeats.12
Relatively large non‐contiguous duplications also lead to deletions, as in the case of the FVIII related gene A (F8A
), which is found in intron 22 of the factor VIII gene and is transcribed in the opposite direction to FVIII. Two further copies of F8A
that are 99.9% identical over 8 kb13
are found approximately 500 kb upstream (telomeric) of the FVIII gene and are transcribed in the same direction as FVIII. Intrachromosomal recombination between F8A
and either of these copies interrupts the factor VIII gene and underlies about half of all cases of severe haemophilia A.14,15
In the region we describe on chromosome 15q15.3, another architectural feature, a large tandem repeat, is present that is prone to rearrangement. A duplicated four‐gene array, which includes KIAA0377
(recently named by HUGO as HISPPD2A
, histidine acid phosphatase domain containing 2A), CKMT1B
and spans 83 kb, is separated by a 10 kb of intermediate unique sequence which contains a 6‐kb LINE sequence.7
These four genes are syntenically conserved among higher mammalian species, including cow, rat, dog, mouse and chimpanzee (based on Genome BLAST, data not shown), however only the human genome includes a duplication, placing its appearance as a recent evolutionary event. Lower vertebrates also do not have STRC
. A comparison of the two duplicated portions shows a 30‐kb region of high sequence homology (99.97% identical) from KIAA0377
(30 kb centromeric) and from pseudo‐KIAA0377
(30 kb telomeric). Using site‐specific nucleotide dosage mapping, we identified a 100‐kb deletion in family D_SM that extended 5′ of centromeric KIAA0377
to 5′ of telomeric pseudo KIAA0377
, deleting all of CKMT1B
(fig 4A). Within the breakpoints lies a pair of imperfect inverted repeats (fig 5A) which are known to promote secondary structure formation.16
This finding suggests that this region is prone to deletions triggered concordantly by inverted repeat pairing and misalignment due to replication slippage between tandem sequences. As shown in fig 5C, the intervening sequence between the transcribed region and the pseudo region forms a loop during replication, allowing the second inverted repeat element in the transcribed region and the first inverted repeat element in the pseudo region to Watson‐Crick base pair with 76% homology (fig 5B).
Figure 5A schematic representation of the breakpoint regions in family D_SM (A) showing the predicted alignments of the two inverted repeats, IR1 and IR2, with 76% base pair matching as predicted by EMBOSS (B), and the resultant (more ...)
The disease phenotype associated with these deletions is characterised by deafness and infertility. Deafness‐infertility syndrome (DIS) was described first by Avidan and colleagues7
in a consanguineous family in which three male siblings had deafness (40‐dB hearing loss involving all frequencies) and infertility (asthenoteratozoospermia). In addition to DIS, congenital dyserythropoietic anaemia type I (CDAI) was also recognised in this family due to a second deletion in another genomic region. The DIS phenotype was attributed to a 70‐kb deletion of chromosome 15q15.3 that included the 5′ region of KIAA0377
(exons 1–24), CKMT1B
and the 3′ region of CATSPER2
(exons 12 and 13). In the three families we studied, the phenotypes in affected persons segregated with deletions of chromosome 15q15. One STRP marker in the deleted interval, D15S784, failed to amplify in all families and may be a useful marker to screen for DIS.
Using site‐specific nucleotide dosage mapping, we found that each family segregated a unique deletion, thus implicating four different deletions with DIS. The hearing loss phenotype is similar by audioprofiling to DFNB16‐related hearing loss, suggesting that deletion of STRC
is causally related to the deafness in DIS, while deletion of CATSPER2
appears to be responsible for the male infertility. Consistent with this hypothesis, the CatSper2‐/‐
mouse mutant is completely infertile in spite of having a normal sperm count and only slightly decreased swimming capacity because sperm cannot transition to the hyperactivated state required for penetration of the zona pellucida.9
The two other genes in the deletion interval, CKMT1
(creatine mitochondrial kinase 1) and KIAA0377
, are both ubiquitously expressed. CKMT1
is present as two transcribed copies, CKMT1A
, which encode the isoenzyme of mitochondrial creatine kinase that is responsible for the transfer of high energy phosphate from mitochondria to creatine in tissues with large fluctuating energy demands. Another isoenzyme in this family is encoded by CKMT2
, the expression of which is limited to sarcomeric tissues of heart and skeletal muscle.17
Deleting only two of four copies of CKMT1
does not give an obvious phenotype, presumably due to functional redundancy.
contains a single histidine acid phosphatase domain with unknown function.7
The large deletions in families L705 and L1014 do not affect the expression of KIAA0377.
However in family D_SM, the 5′ portion of KIAA0377
(5′UTR to exon 3) is replaced by its counterpart in ΨKIAA0377
. Over the replacement interval, KIAA0377
differ by only one nucleotide (intron 2, SMN8), and hence the expression of KIAA0377
would be predicted to be unaltered. We confirmed this prediction by demonstrating KIAA0377
mRNA transcripts in all affected individuals by RT‐PCR amplification and direct sequencing (the primers target exon 3 and exon 5) (fig 4A).
In summary, we have identified three families segregating an autosomal recessive contiguous gene deletion syndrome characterised by deafness and sperm dysmotility. This new syndrome is caused by the deletion of contiguous genes at 15q15.3. The region contains a pair of imperfect inverted repeats, which are known to promote secondary structure formation, and suggests that the deletion is triggered concordantly by inverted repeat pairing and misalignment due to replication slippage between tandem sequences.