ZFIN is now using GRCz12tu for Genomic Data
Gene
smchd1
- ID
- ZDB-GENE-050211-6
- Name
- structural maintenance of chromosomes flexible hinge domain containing 1
- Symbol
- smchd1 Nomenclature History
- Previous Names
-
- kiaa0650l
- Type
- protein_coding_gene
- Location
- Chr: 7 Mapping Details/Browsers
- Genome Assembly
- GRCz12tu
- Annotation Status
- Current
- Description
- Acts upstream of or within with a positive effect on definitive hemopoiesis. Acts upstream of or within bone development and embryonic cranial skeleton morphogenesis. Predicted to be located in chromosome. Is expressed in head; hematopoietic system; mesoderm; and oocyte. Used to study choanal atresia. Human ortholog(s) of this gene implicated in facioscapulohumeral muscular dystrophy 2. Orthologous to human SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1).
- Genome Resources
- Note
- None
- Comparative Information
-
- All Expression Data
- 7 figures from 4 publications
- Cross-Species Comparison
- High Throughput Data
- Thisse Expression Data
- No data available
Wild Type Expression Summary
Phenotype Summary
Mutations
| Allele | Type | Localization | Consequence | Mutagen | Supplier |
|---|---|---|---|---|---|
| ns301 | Allele with one deletion | Exon 4 | Unknown | CRISPR | |
| ns302 | Allele with one delins | Exon 4 | Unknown | CRISPR | |
| ns303 | Allele with one insertion | Exon 4 | Unknown | CRISPR | |
| sa18180 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa27111 | Allele with one point mutation | Unknown | Premature Stop | ENU | |
| sa34256 | Allele with one point mutation | Unknown | Premature Stop | ENU |
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| Targeting Reagent | Created Alleles | Citations |
|---|---|---|
| CRISPR1-smchd1 | (2) | |
| CRISPR2-smchd1 | Mooney et al., 2019 | |
| CRISPR3-smchd1 | Xue et al., 2022 | |
| MO1-smchd1 | N/A | (2) |
| MO2-smchd1 | N/A | Shaw et al., 2017 |
| MO3-smchd1 | N/A | Xue et al., 2019 |
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Human Disease
| Disease Ontology Term | Multi-Species Data | OMIM Term | OMIM Phenotype ID |
|---|---|---|---|
| facioscapulohumeral muscular dystrophy 2 | Alliance | Facioscapulohumeral muscular dystrophy 2, digenic | 158901 |
| Bosma arhinia microphthalmia syndrome | 603457 |
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| Human Disease | Fish | Conditions | Citations |
|---|---|---|---|
| choanal atresia | zf195Tg + CRISPR1-smchd1 (AB) | standard conditions | Shaw et al., 2017 |
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Domain, Family, and Site Summary
| Type | InterPro ID | Name |
|---|---|---|
| Domain | IPR010935 | SMCs flexible hinge |
| Domain | IPR055109 | SMCHD1, ribosomal S5 domain 2-like domain |
| Family | IPR038892 | Structural maintenance of chromosomes flexible hinge domain-containing protein 1 |
| Homologous_superfamily | IPR036277 | SMCs flexible hinge superfamily |
| Homologous_superfamily | IPR036890 | Histidine kinase/HSP90-like ATPase superfamily |
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Domain Details Per Protein
| Protein | Additional Resources | Length | Histidine kinase/HSP90-like ATPase superfamily | SMCHD1, ribosomal S5 domain 2-like domain | SMCs flexible hinge | SMCs flexible hinge superfamily | Structural maintenance of chromosomes flexible hinge domain-containing protein 1 |
|---|---|---|---|---|---|---|---|
| UniProtKB:A0A8M3AUP8 | InterPro | 1983 |
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| Type | Name | Annotation Method | Has Havana Data | Length (nt) | Analysis |
|---|---|---|---|---|---|
| mRNA |
smchd1-201
(1)
|
Ensembl | 6,420 nt |
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Interactions and Pathways
No data available
Plasmids
No data available
No data available
| Relationship | Marker Type | Marker | Accession Numbers | Citations |
|---|---|---|---|---|
| Contained in | BAC | CH73-310J3 | ZFIN Curated Data |
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| Type | Accession # | Genome Assembly | Length (nt/aa) | Analysis |
|---|---|---|---|---|
| RNA | RefSeq:XM_073907573 (1) | GRCz12tu | 7552 nt | |
| Genomic | GenBank:FP016237 (1) | 90568 nt | ||
| Polypeptide | UniProtKB:A0A8M3AUP8 (1) | 1983 aa |
- Comparative Orthology
- Alliance
- Xue, S., Ly, T.T.N., Vijayakar, R.S., Chen, J., Ng, J., Mathuru, A.S., Magdinier, F., Reversade, B. (2022) HOX epimutations driven by maternal SMCHD1/LRIF1 haploinsufficiency trigger homeotic transformations in genetically wildtype offspring. Nature communications. 13:3583
- Mooney, M.R., Davis, E.E., Katsanis, N. (2019) Analysis of Single Nucleotide Variants in CRISPR-Cas9 Edited Zebrafish Exomes Shows No Evidence of Off-Target Inflation. Frontiers in genetics. 10:949
- Xue, Y., Liu, D., Cui, G., Ding, Y., Ai, D., Gao, S., Zhang, Y., Suo, S., Wang, X., Lv, P., Zhou, C., Li, Y., Chen, X., Peng, G., Jing, N., Han, J.J., Liu, F. (2019) A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis. Cell Reports. 27:1567-1578.e5
- Shaw, N.D., Brand, H., Kupchinsky, Z.A., Bengani, H., Plummer, L., Jones, T.I., Erdin, S., Williamson, K.A., Rainger, J., Stortchevoi, A., Samocha, K., Currall, B.B., Dunican, D.S., Collins, R.L., Willer, J.R., Lek, A., Lek, M., Nassan, M., Pereira, S., Kammin, T., Lucente, D., Silva, A., Seabra, C.M., Chiang, C., An, Y., Ansari, M., Rainger, J.K., Joss, S., Smith, J.C., Lippincott, M.F., Singh, S.S., Patel, N., Jing, J.W., Law, J.R., Ferraro, N., Verloes, A., Rauch, A., Steindl, K., Zweier, M., Scheer, I., Sato, D., Okamoto, N., Jacobsen, C., Tryggestad, J., Chernausek, S., Schimmenti, L.A., Brasseur, B., Cesaretti, C., García-Ortiz, J.E., Buitrago, T.P., Silva, O.P., Hoffman, J.D., Mühlbauer, W., Ruprecht, K.W., Loeys, B.L., Shino, M., Kaindl, A.M., Cho, C.H., Morton, C.C., Meehan, R.R., van Heyningen, V., Liao, E.C., Balasubramanian, R., Hall, J.E., Seminara, S.B., Macarthur, D., Moore, S.A., Yoshiura, K.I., Gusella, J.F., Marsh, J.A., Graham, J.M., Lin, A.E., Katsanis, N., Jones, P.L., Crowley, W.F., Davis, E.E., FitzPatrick, D.R., Talkowski, M.E. (2017) SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome. Nature Genetics. 49(2):238-248
- Briolat, V., Jouneau, L., Carvalho, R., Palha, N., Langevin, C., Herbomel, P., Schwartz, O., Spaink, H.P., Levraud, J.P., Boudinot, P. (2014) Contrasted Innate Responses to Two Viruses in Zebrafish: Insights into the Ancestral Repertoire of Vertebrate IFN-Stimulated Genes. Journal of immunology (Baltimore, Md. : 1950). 192:4328-41
- Galloway, J.L., Wingert, R.A., Thisse, C., Thisse, B., and Zon, L.I. (2008) Combinatorial regulation of novel erythroid gene expression in zebrafish. Experimental hematology. 36(4):424-432
- Galloway, J.L., Wingert, R.A., Thisse, C., Thisse, B., and Zon, L.I. (2005) Loss of gata1 but not gata2 converts erythropoiesis to myelopoiesis in zebrafish embryos. Developmental Cell. 8(1):109-116
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