Alternative titles; symbols
HGNC Approved Gene Symbol: COL4A6
Cytogenetic location: Xq22.3 Genomic coordinates (GRCh38): X:108,155,614-108,439,458 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| Xq22.3 | ?Deafness, X-linked 6 | 300914 | X-linked recessive | 3 |
The COL4A6 gene encodes the collagen type IV alpha-6 isoform, which is a component of the basement membrane. Basement membranes compartmentalize tissues and provide important signals for the differentiation of the cells they support. Type IV collagen, the major component of basement membranes, is a triple-helical molecule composed of 3 alpha chains. The alpha-1 (COL4A1; 120130) and alpha-2 (COL4A2; 120090) chains are ubiquitous, whereas the alpha-3 (COL4A3; 120070), alpha-4 (COL4A4; 120131) and alpha-5 (COL4A5; 303630) chains have restricted tissue distributions. On the basis of sequence similarities, the chains fall into 2 classes: alpha-1, alpha-3, and alpha-5 compose the alpha-1-like class, and alpha-2, alpha-4, and alpha-6 compose the alpha-2-like class. The COL4A1 and COL4A2 genes are located in a head-to-head configuration on chromosome 13 and the COL4A3 and COL4A4 genes are similarly arranged on chromosome 2. Thus, it appears that the type IV collagens evolved by duplication of an ancestral alpha-chain gene, giving rise to a pair of alpha-chain genes with closely apposed 5-prime ends (Oohashi et al., 1994; Zhou et al., 1994).
From an analysis of cDNAs, Oohashi et al. (1994) deduced the primary structure of the alpha-6 chain of collagen type IV. The deduced polypeptide contains 1,678 amino acid residues, including a 21-residue signal peptide, a 24-residue amino-terminal noncollagenous domain, a central 1,405-residue collagenous domain, and a 228-residue carboxy-terminal noncollagenous domain.
Zhou et al. (1994) described the entire human COL4A6 cDNA and showed that the gene encodes a classic type IV collagen with homology throughout its length to the other 5 chains. There is a 21-residue signal peptide, a 1,417-residue collagenous domain (note different length from that given by Oohashi et al., 1994) interrupted at 25 points, and a 228-residue carboxy-terminal noncollagenous domain. Its structure most closely resembled that of COL4A2 and COL4A4. Zhou et al. (1994) deduced the evolution of the 6 chains, allowing a new classification of the type IV collagen family.
Sugimoto et al. (1994) described the 5-prime flanking sequence of COL4A5 and COL4A6. Analysis of the sequence immediately upstream of the transcription start sites revealed features of housekeeping genes, namely, the lack of a TATA motif and the presence of CCAAT and CTC boxes. Furthermore, the COL4A6 gene was found to contain 2 alternative promoters that control the generation of 2 different transcripts. One transcription start site (from exon 1-prime) is 442 bp away from the transcription start site of COL4A5, while an alternative transcription start site (from exon 1) is located 1,050 bp from the first one and drives the expression of a second transcript that encodes an alpha-6(IV) chain with a different signal peptide. Reverse transcription-PCR experiments revealed that the transcript from exon 1-prime is abundant in placenta, whereas the transcript from exon 1 is more frequently found in kidney and lung. These results provided additional clues to the mechanism used in generating unique basement membrane structures in different tissues.
By immunohistochemical staining, Rost et al. (2014) found expression of the Col4a6 gene in the mouse inner ear, most pronounced in membranous and osseous structures at the stria vascularis of the spiral ligament, as well as in a subgroup of ganglia cells. Zebrafish embryos showed dynamic expression of Col4a6 in the nervous system and ear, particularly the otic vesicle.
By immunohistochemical analysis, Tang et al. (2021) showed that Col4a6 protein was distributed throughout mouse cochlea within subepithelial basement membranes underlying interdental cells, inner sulcus cells, basilar membrane, outer sulcus cells, root cells, and Reissner membrane, and in perivascular basement membranes in the spiral limbus, spiral ligament, and stria vascularis.
Oohashi et al. (1995) determined that the human COL4A6 gene spans over 200 kb and contains 46 exons. Exons 1-prime and 1 encode the two different 5-prime UTRs and the 2 amino-terminal parts of the signal peptide. Oohashi et al. (1995) identified 3 CA repeat markers within COL4A6 that could be used for allele detection, linkage analysis, and familial diagnosis of diseases caused by mutations in this gene.
Zhang et al. (1996) described the complete exon/intron size pattern of the COL4A6 gene, which spans about 425 kb. They studied 85 kb of the gene and 25 kb of flanking sequences, including all 46 exons of the gene and all introns, except intron 2. Intron 2 was deduced to be about 340 kb in size. They found that the exon size pattern of COL4A6 is highly homologous with that of the human and mouse COL4A2 genes, with 27 of the 46 exons of COL4A6 being identical in size between the genes.
Oohashi et al. (1994) mapped the COL4A6 gene to chromosome Xq22 by in situ hybridization.
Zhou et al. (1993) predicted that the COL4A5 gene might be paired with an alpha-2-like gene; indeed, they proved that this was the case, demonstrating a COL4A6 gene located on the X chromosome in a head-to-head arrangement and within 452 bp of the COL4A5 gene (303630).
In 4 affected male members of a Hungarian family with congenital X-linked deafness-6 (DFNX6; 300914), Rost et al. (2014) identified a hemizygous mutation in the COL4A6 gene (G591S; 303631.0002). Five female heterozygous mutation carriers developed mild hearing loss, and 1 female mutation carrier was unaffected at age 46 years. The mutation was found by exome sequencing of the X chromosome. Sequencing of the COL4A6 gene in 96 additional patients with hearing loss did not identify any mutations.
By next-generation sequencing on a 187-gene hearing loss panel, O'Brien et al. (2022) identified 2 families in which members had congenital deafness and variants in the COL4A6 gene. In family A, the proband was hemizygous for a maternally inherited donor splice site variant for exon 15 (c.951+1G-T). A splicing assay revealed skipping of exon 15 with introduction of an early stop codon, suggesting that the variant is likely pathogenic. The variant had a minor allele frequency of 0.00001 in gnomAD. However, the proband also inherited a pathogenic heterozygous mutation in the GJB2 gene (R75W; 121011.0011) from his affected father. The authors hypothesized that both the COL4A6 and GJB2 variants contributed to the hearing loss in the proband being more severe than that seen in his parents, but audiometric data were not available to prove this hypothesis. In family B, ascertained from an audiology clinic in Mexico, 4 family members had severe to profound hearing loss of prelingual onset. In the proband (B-III-1), no causative mutation was identified. However, in the proband's father, paternal uncle, and paternal grandmother, the author's identified a missense mutation in the COL4A6 gene (G1091A; 303631.0003) that disrupts the Gly-X-Y motif. The variant was rare in the Latino population according to gnomAD (0.001075). According to ACMG criteria, this variant is classified as a variant of uncertain significance.
The X-linked form of Alport syndrome (ATS; 301050) results from mutations in the COL4A5 gene (303630). Zhou et al. (1993) found that when deletions in COL4A5 extend into the neighboring COL4A6 gene, ATS may be accompanied by diffuse leiomyomatosis (DL) in the esophagus (ATS-DL; 308940). This is a clear example of a 'contiguous gene syndrome.' Zhou et al. (1993) concluded that the COL4A6 gene and its product are critical for normal smooth muscle differentiation. Although the authors suggested that some patients with isolated Alport syndrome may also have COL4A6 mutations, Southern blot analysis in a large number of ATS patients excluded an abnormal pattern.
Heidet et al. (1995) showed that the deletion of the COL4A5 and COL4A6 genes observed in 7 patients with diffuse leiomyomatosis/Alport syndrome complex encompasses only the first 2 exons of COL4A6, with a breakpoint located in the second intron of COL4A6, the size of which exceeds 65 kb. Three patients with ATS without leiomyomatosis and with a deletion of the 5-prime part of the COL4A5 gene displayed a larger deletion of COL4A6. Moreover, a COL4A6 mRNA product was detected by RT-PCR in an esophageal tumor sample of a patient with diffuse leiomyomatosis/Alport syndrome complex. These results suggest that the contiguous gene syndrome is caused by an abnormal truncated alpha-6(IV) chain.
Larger genetic lesions that completely eliminate both collagen genes present only with ATS. A critical region of COL4A6, including some of its third intron, needs to be spared for leiomyomatosis to occur. It had been proposed that this intron contains structural or regulatory elements of a third, as yet unidentified gene that represses DL; alternatively, a truncated form of COL4A6 may affect smooth muscle cell growth directly. Ueki et al. (1998) studied a 19-year-old boy who, at the age of 6 years, was found to have hematuria accompanied by kidney biopsy findings consistent with Alport syndrome. At the age of 8 years, he developed esophageal dysfunction and underwent esophageal gastrectomy. Studies of the COL4A6/COL4A5 region suggested a 17-kb deletion extending from 3-prime of the third PstI site of intron 3 of COL4A6 to immediately 5-prime of the BamHI site of intron 1 of COL4A5. Since the 2 genes are oriented head-to-head, the deletion eliminated the first coding exon of COL4A5 and the first 2 coding exons of COL4A6. Ueki et al. (1998) found that the breakpoints shared the same sequence, which, in turn, was closely homologous to the consensus sequences of topoisomerases I (TOP1; 126420) and II (TOP2; 126430). Additional DNA evidence suggested that the patient was a somatic mosaic for the mutation. Immunohistochemical analysis using alpha-chain-specific monoclonal antibodies supported this conclusion, since it revealed the absence of the alpha-5 and alpha-6 chains of collagen IV in most but not all of the basement membranes of the smooth muscle cell tumor. They also documented a similar segmental staining pattern in the glomerular basement membranes of the patient's kidney. The presence of multiple consensus sequences of topoisomerases surrounding the breakpoints may suggest a mechanism for somatic deletion in the COL4A5/COL4A6 region, but the reason for phenotypic differences between short and long COL4A6 deletions remained unknown.
Tang et al. (2021) found that Col4a6 -/- mice had normal hearing threshold and normal cochlear structures, with no change in distribution of major basement membrane components. Thus, deletion of Col4a6 in mice did not recapitulate the congenital hearing loss observed in humans with the COL4A6 gly591-to-ser (G591S; 303631.0002) mutation.
In 4 affected male members of a Hungarian family with X-linked deafness-6 (DFNX6; 300914), Rost et al. (2014) identified a hemizygous c.1771G-A transition in exon 23 of the COL4A6 gene, resulting in a gly591-to-ser (G591S) substitution at a highly conserved residue. The mutation, which was found by X-chromosomal exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was not present in 407 ethnically matched controls or in public SNP databases. Four female heterozygous mutation carriers developed mild hearing loss with age, 1 female carrier had mild hearing loss at age 9 years, and another female carrier was unaffected at age 46 years. None of the mutation carriers had renal or ocular abnormalities. The location of the G591S substitution at a highly conserved glycine residue within the triple helix structure was predicted to destabilize the whole collagen molecule. Functional studies of the variant were not performed.
This variant is classified as a variant of unknown significance because it is classified as such by ACMG criteria. In addition, of the 4 family members with nonsyndromic hearing loss reported by O'Brien et al. (2022), the variant was identified in only 3 members; no causative variant was identified in the proband.
O'Brien et al. (2022) reported a family (family B) in which 4 members had severe to profound nonsyndromic hearing loss of prelingual onset. No causative mutation was identified in the proband (III:1), but his affected father (II:3), paternal uncle (II:2), and paternal grandmother (I:2) were found to have a c.3272G-C transition (c.3272G-C, NM_001287758.1) in the COL4A6 gene, resulting in a gly1091-to-ala (G1091A) substitution that disrupts the Gly-X-Y motif. The variant was rare in the Latino population in the gnomAD database (MAF of 0.001075). No functional studies were reported.
Heidet, L., Dahan, K., Zhou, J., Xu, Z., Cochat, P., Gould, J. D. M., Leppig, K. A., Proesmans, W., Guyot, C., Guillot, M., Roussel, B., Tryggvason, K., Grunfeld, J.-P., Gubler, M.-C., Antignac, C. Deletions of both alpha-5(IV) and alpha-6(IV) collagen genes in Alport syndrome and in Alport syndrome associated with smooth muscle tumours. Hum. Molec. Genet. 4: 99-108, 1995. [PubMed: 7711741] [Full Text: https://doi.org/10.1093/hmg/4.1.99]
O'Brien, A., Aw, W. Y., Tee, H. Y., Naegeli, K. M., Bademci, G., Tekin, M., Arnos, K., Pandya, A. Confirmation of COL4A6 variants in X-linked nonsyndromic hearing loss and its clinical implications. Europ. J. Hum. Genet. 30: 7-12, 2022. [PubMed: 33840813] [Full Text: https://doi.org/10.1038/s41431-021-00881-2]
Oohashi, T., Sugimoto, M., Mattei, M.-G., Ninomiya, Y. Identification of a new collagen IV chain, alpha-6(IV), by cDNA isolation and assignment of the gene to chromosome Xq22, which is the same locus for COL4A5. J. Biol. Chem. 269: 7520-7526, 1994. [PubMed: 8125972]
Oohashi, T., Ueki, Y., Sugimoto, M., Ninomiya, Y. Isolation and structure of the COL4A6 gene encoding the human alpha-6(IV) collagen chain and comparison with other type IV collagen genes. J. Biol. Chem. 270: 26863-26867, 1995. [PubMed: 7592929] [Full Text: https://doi.org/10.1074/jbc.270.45.26863]
Rost, S., Bach, E., Neuner, C., Nanda, I., Dysek, S., Bittner, R. E., Keller, A., Bartsch, O., Mlynski, R., Haaf, T., Muller, C. R., Kunstmann, E. Novel form of X-linked nonsyndromic hearing loss with cochlear malformation caused by a mutation in the type IV collagen gene COL4A6. Europ. J. Hum. Genet. 22: 208-215, 2014. [PubMed: 23714752] [Full Text: https://doi.org/10.1038/ejhg.2013.108]
Sugimoto, M., Oohashi, T., Ninomiya, Y. The genes COL4A5 and COL4A6, coding for basement membrane collagen chains alpha-5(IV) and alpha-6(IV), are located head-to-head in close proximity on human chromosome Xq22 and COL4A6 is transcribed from two alternative promoters. Proc. Nat. Acad. Sci. 91: 11679-11683, 1994. [PubMed: 7972123] [Full Text: https://doi.org/10.1073/pnas.91.24.11679]
Tang, S., Yonezawa, T., Maeda, Y., Ono, M., Maeba, T., Miyoshi, T., Momota, R., Tomono, Y., Oohashi, T. Lack of collagen alpha-6(IV) chain in mice does not cause severe-to-profound hearing loss or cochlear malformation, a distinct phenotype from nonsyndromic hearing loss with COL4A6 missense mutation. PLoS One 16: e0249909, 2021. [PubMed: 33848312] [Full Text: https://doi.org/10.1371/journal.pone.0249909]
Ueki, Y., Naito, I., Oohashi, T., Sugimoto, M., Seki, T., Yoshioka, H., Sado, Y., Sato, H., Sawai, T., Sasaki, F., Matsuoka, M., Fukuda, S., Ninomiya, Y. Topoisomerase I and II consensus sequences in a 17-kb deletion junction of the COL4A5 and COL4A6 genes and immunohistochemical analysis of esophageal leiomyomatosis associated with Alport syndrome. Am. J. Hum. Genet. 62: 253-261, 1998. [PubMed: 9463311] [Full Text: https://doi.org/10.1086/301703]
Zhang, X., Zhou, J., Reeders, S. T., Tryggvason, K. Structure of the human type IV collagen COL4A6 gene, which is mutated in Alport syndrome-associated leiomyomatosis. Genomics 33: 473-479, 1996. [PubMed: 8661006] [Full Text: https://doi.org/10.1006/geno.1996.0222]
Zhou, J., Ding, M., Zhao, Z., Reeders, S. T. Complete primary structure of the sixth chain of human basement membrane collagen, alpha-6(IV): isolation of the cDNAs for alpha-6(IV) and comparison with five other type IV collagen chains. J. Biol. Chem. 269: 13193-13199, 1994. [PubMed: 8175748]
Zhou, J., Mochizuki, T., Smeets, H., Antignac, C., Laurila, P., de Paepe, A., Tryggvason, K., Reeders, S. T. Deletion of the paired alpha-5(IV) and alpha-6(IV) collagen genes in inherited smooth muscle tumors. Science 261: 1167-1169, 1993. [PubMed: 8356449] [Full Text: https://doi.org/10.1126/science.8356449]