| Name | family with sequence similarity 9, member A |
| Description | This gene is a member of a gene family which arose through duplication on the X chromosome. The encoded protein may be a nuclear protein that is localized to the nucleolus, and has some similarity to a synaptonemal complex protein. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Aug 2011] |
| Summary |
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n FAM9A is an X‐linked gene that appears to play roles in reproductive and developmental processes. It belongs to a family of genes (including FAM9B and FAM9C) that are expressed exclusively in the testis, with immunohistochemical studies demonstrating a nuclear localization and, in the case of FAM9A, even a specific enrichment in the nucleolus."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": " The deduced amino acid sequence shows homology to SYCP3, a key component of the synaptonemal complex during meiosis, suggesting that FAM9A may be involved in chromosomal pairing or recombination events during germ cell development."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In pathological contexts, altered expression or copy number variations involving FAM9A have been implicated in reproductive disorders. For instance, in testicular samples from patients with Klinefelter syndrome, FAM9A marks undifferentiated somatic cell populations, which may indicate a role in the proper maturation of gonadal cells."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": " Similarly, deletions or duplications that include FAM9A have been observed in cases of Kallmann syndrome, suggesting that perturbations of this genomic region might indirectly affect gonadotropin regulation and spermatogenesis."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Beyond its functions in the testis, genetic association studies have identified the FAM9A/FAM9B locus as a male‐specific susceptibility region for inguinal hernia, further highlighting the importance of this genomic region in sex‐related phenotypes."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": " In addition, epigenetic analyses in uterine leiomyomas have revealed that FAM9A is among a set of X‐chromosome genes with aberrant hypomethylation, suggesting that dysregulation of FAM9A expression may also have implications in hormonally regulated tissues outside the testis."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Collectively, these observations propose that FAM9A is involved in key meiotic processes and testicular cell differentiation, while its altered dosage or epigenetic status may contribute to male-biased clinical conditions and developmental syndromes.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Isabel Martinez-Garay, Sibylle Jablonka, Marketa Sutajova, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A new gene family (FAM9) of low-copy repeats in Xp22.3 expressed exclusively in testis: implications for recombinations in this region."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genomics (2002)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1006/geno.2002.6834"}], "href": "https://doi.org/10.1006/geno.2002.6834"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12213195"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12213195"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Sofia Boeg Winge, Marlene Danner Dalgaard, Kirstine G Belling, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Transcriptome analysis of the adult human Klinefelter testis and cellularity-matched controls reveals disturbed differentiation of Sertoli- and Leydig cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Death Dis (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41419-018-0671-1"}], "href": "https://doi.org/10.1038/s41419-018-0671-1"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29789566"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29789566"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Nina Prepeluh, Bojan Korpar, Andreja Zagorac, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A mosaic form of microphthalmia with linear skin defects."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "BMC Pediatr (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s12887-018-1234-4"}], "href": "https://doi.org/10.1186/s12887-018-1234-4"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30068298"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30068298"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Y Niu, C Zhou, H Xu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Novel interstitial deletion in Xp22.3 in a typical X-linked recessive family with Kallmann syndrome."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Andrologia (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/and.12961"}], "href": "https://doi.org/10.1111/and.12961"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29441621"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29441621"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Hélène Choquet, Weiyu Li, Jie Yin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Ancestry- and sex-specific effects underlying inguinal hernia susceptibility identified in a multiethnic genome-wide association study meta-analysis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Mol Genet (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/hmg/ddac003"}], "href": "https://doi.org/10.1093/hmg/ddac003"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "35022708"}], "href": "https://pubmed.ncbi.nlm.nih.gov/35022708"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Ryo Maekawa, Shintaro Yagi, Jun Ohgane, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Disease-dependent differently methylated regions (D-DMRs) of DNA are enriched on the X chromosome in uterine leiomyoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Reprod Dev (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1262/jrd.11-035a"}], "href": "https://doi.org/10.1262/jrd.11-035a"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21685710"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21685710"}]}]}]}
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| Synonyms | TEX39A |
| Proteins | FAM9A_HUMAN |
| NCBI Gene ID | 171482 |
| API | |
| Download Associations | |
| Predicted Functions |
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| Co-expressed Genes |
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| Expression in Tissues and Cell Lines |
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FAM9A has 921 functional associations with biological entities spanning 7 categories (molecular profile, functional term, phrase or reference, chemical, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 51 datasets.
Click the + buttons to view associations for FAM9A from the datasets below.
If available, associations are ranked by standardized value
| Dataset | Summary | |
|---|---|---|
| Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles | tissue samples with high or low expression of FAM9A gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset. | |
| Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray | tissue samples with high or low expression of FAM9A gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset. | |
| CCLE Cell Line Gene CNV Profiles | cell lines with high or low copy number of FAM9A gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset. | |
| CCLE Cell Line Gene Expression Profiles | cell lines with high or low expression of FAM9A gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset. | |
| ChEA Transcription Factor Targets 2022 | transcription factors binding the promoter of FAM9A gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset. | |
| CM4AI KOLF21J CRISPRi Gene Perturbation Atlas | gene perturbations changing expression of FAM9A gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset. | |
| COMPARTMENTS Curated Protein Localization Evidence Scores | cellular components containing FAM9A protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset. | |
| COMPARTMENTS Curated Protein Localization Evidence Scores 2025 | cellular components containing FAM9A protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset. | |
| COMPARTMENTS Text-mining Protein Localization Evidence Scores | cellular components co-occuring with FAM9A protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset. | |
| COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 | cellular components co-occuring with FAM9A protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset. | |
| COSMIC Cell Line Gene CNV Profiles | cell lines with high or low copy number of FAM9A gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset. | |
| COSMIC Cell Line Gene Mutation Profiles | cell lines with FAM9A gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset. | |
| CTD Gene-Chemical Interactions | chemicals interacting with FAM9A gene/protein from the curated CTD Gene-Chemical Interactions dataset. | |
| DepMap CRISPR Gene Dependency | cell lines with fitness changed by FAM9A gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset. | |
| DISEASES Experimental Gene-Disease Association Evidence Scores | diseases associated with FAM9A gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores dataset. | |
| DISEASES Text-mining Gene-Disease Association Evidence Scores | diseases co-occuring with FAM9A gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset. | |
| DISEASES Text-mining Gene-Disease Association Evidence Scores 2025 | diseases co-occuring with FAM9A gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset. | |
| DisGeNET Gene-Disease Associations | diseases associated with FAM9A gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset. | |
| ENCODE Histone Modification Site Profiles | histone modification site profiles with high histone modification abundance at FAM9A gene from the ENCODE Histone Modification Site Profiles dataset. | |
| ENCODE Transcription Factor Binding Site Profiles | transcription factor binding site profiles with transcription factor binding evidence at the promoter of FAM9A gene from the ENCODE Transcription Factor Binding Site Profiles dataset. | |
| ENCODE Transcription Factor Targets | transcription factors binding the promoter of FAM9A gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset. | |
| GeneRIF Biological Term Annotations | biological terms co-occuring with FAM9A gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset. | |
| GeneSigDB Published Gene Signatures | PubMedIDs of publications reporting gene signatures containing FAM9A from the GeneSigDB Published Gene Signatures dataset. | |
| GEO Signatures of Differentially Expressed Genes for Gene Perturbations | gene perturbations changing expression of FAM9A gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset. | |
| GEO Signatures of Differentially Expressed Genes for Kinase Perturbations | kinase perturbations changing expression of FAM9A gene from the GEO Signatures of Differentially Expressed Genes for Kinase Perturbations dataset. | |
| GO Biological Process Annotations 2023 | biological processes involving FAM9A gene from the curated GO Biological Process Annotations 2023 dataset. | |
| GO Biological Process Annotations 2025 | biological processes involving FAM9A gene from the curated GO Biological Process Annotations2025 dataset. | |
| GO Cellular Component Annotations 2015 | cellular components containing FAM9A protein from the curated GO Cellular Component Annotations 2015 dataset. | |
| GO Molecular Function Annotations 2015 | molecular functions performed by FAM9A gene from the curated GO Molecular Function Annotations 2015 dataset. | |
| GTEx Tissue Gene Expression Profiles | tissues with high or low expression of FAM9A gene relative to other tissues from the GTEx Tissue Gene Expression Profiles dataset. | |
| GTEx Tissue Gene Expression Profiles 2023 | tissues with high or low expression of FAM9A gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset. | |
| GWAS Catalog SNP-Phenotype Associations 2025 | phenotypes associated with FAM9A gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset. | |
| Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles | cell lines with high or low expression of FAM9A gene relative to other cell lines from the Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles dataset. | |
| HPA Tissue Protein Expression Profiles | tissues with high or low expression of FAM9A protein relative to other tissues from the HPA Tissue Protein Expression Profiles dataset. | |
| InterPro Predicted Protein Domain Annotations | protein domains predicted for FAM9A protein from the InterPro Predicted Protein Domain Annotations dataset. | |
| JASPAR Predicted Human Transcription Factor Targets 2025 | transcription factors regulating expression of FAM9A gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset. | |
| JASPAR Predicted Transcription Factor Targets | transcription factors regulating expression of FAM9A gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Transcription Factor Targets dataset. | |
| Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles | cell lines with high or low copy number of FAM9A gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset. | |
| KnockTF Gene Expression Profiles with Transcription Factor Perturbations | transcription factor perturbations changing expression of FAM9A gene from the KnockTF Gene Expression Profiles with Transcription Factor Perturbations dataset. | |
| LOCATE Predicted Protein Localization Annotations | cellular components predicted to contain FAM9A protein from the LOCATE Predicted Protein Localization Annotations dataset. | |
| NURSA Protein Complexes | protein complexs containing FAM9A protein recovered by IP-MS from the NURSA Protein Complexes dataset. | |
| Pathway Commons Protein-Protein Interactions | interacting proteins for FAM9A from the Pathway Commons Protein-Protein Interactions dataset. | |
| Roadmap Epigenomics Histone Modification Site Profiles | histone modification site profiles with high histone modification abundance at FAM9A gene from the Roadmap Epigenomics Histone Modification Site Profiles dataset. | |
| Rummagene Transcription Factor Associations 2026 | transcription factors regulating expression of FAM9A gene from the Rummagene Transcription Factor Associations 2026 dataset. | |
| RummaGEO Drug Perturbation Signatures | drug perturbations changing expression of FAM9A gene from the RummaGEO Drug Perturbation Signatures dataset. | |
| RummaGEO Gene Perturbation Signatures | gene perturbations changing expression of FAM9A gene from the RummaGEO Gene Perturbation Signatures dataset. | |
| TargetScan Predicted Nonconserved microRNA Targets | microRNAs regulating expression of FAM9A gene predicted using nonconserved miRNA seed sequences from the TargetScan Predicted Nonconserved microRNA Targets dataset. | |
| TCGA Signatures of Differentially Expressed Genes for Tumors | tissue samples with high or low expression of FAM9A gene relative to other tissue samples from the TCGA Signatures of Differentially Expressed Genes for Tumors dataset. | |
| TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 | tissues with high expression of FAM9A protein in proteomics datasets from the TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 dataset. | |
| TISSUES Text-mining Tissue Protein Expression Evidence Scores | tissues co-occuring with FAM9A protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores dataset. | |
| TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 | tissues co-occuring with FAM9A protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset. | |
