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Gene

KDM6B

lysine demethylase 6B

Summary

Cytogenetic location
17p13.1
Coordinates
Chromosome 17: 7,834,217–7,854,796 (GRCh38)
Exons
24 exons across 20.6 kb
Protein
1,643 amino acids
Also known as
KIAA0346
Previous symbols
JMJD3
MANE Select transcript
ENST00000448097.7NM_001348716.2
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

    • Intellectual Disability

      • One of 233 genes linked to it

        • ClinGen rates the link definitive
        • 1 GenCC submitter rates it definitive or strong

    How KDM6B is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    Chromosome 17, with a bracket where KDM6B sits. KDM6B and 61 genes near it on chromosome 17, from 7,344,507 to 8,344,506.Chromosome 1717p13.1p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.37.4 Mb7.6 Mb7.8 Mb8 Mb8.2 MbACAP1: 7,332,960–7,351,478, forward strandKCTD11: 7,351,889–7,354,944, forward strandKCTD11TMEM95: 7,355,123–7,357,219, forward strandTMEM95TNK1: 7,380,534–7,389,779, forward strandTNK1PLSCR3: 7,389,727–7,397,054, reverse strandPLSCR3TMEM256-PLSCR3: 7,389,734–7,404,097, reverse strandTMEM256: 7,402,774–7,404,138, reverse strandNLGN2: 7,404,684–7,419,860, forward strandSPEM1: 7,420,323–7,421,637, forward strandSPEM2: 7,425,563–7,427,568, forward strandSPEM3: 7,428,857–7,432,820, forward strand: 7,428,861–7,436,278, forward strandTMEM102: 7,435,344–7,437,679, forward strandFGF11: 7,438,128–7,444,937, forward strandFGF11CHRNB1: 7,445,004–7,457,710, forward strandCHRNB1ZBTB4: 7,459,366–7,484,278, reverse strandZBTB4SLC35G6: 7,481,446–7,483,496, forward strandSLC35G6POLR2A: 7,484,366–7,514,616, forward strandPOLR2ATNFSF12: 7,548,508–7,557,890, forward strandTNFSF12-TNFSF13: 7,549,099–7,561,601, forward strandTNFSF13: 7,558,251–7,561,660, forward strandSENP3: 7,561,867–7,571,969, forward strandSENP3-EIF4A1: 7,563,287–7,578,715, forward strandEIF4A1: 7,572,718–7,579,007, forward strandCD68: 7,579,380–7,582,515, forward strandMPDU1: 7,583,214–7,594,419, forward strandSOX15: 7,588,178–7,590,101, reverse strandSOX15FXR2: 7,591,230–7,614,916, reverse strandFXR2SHBG: 7,613,946–7,633,469, forward strandSHBGSAT2: 7,626,234–7,627,879, reverse strandSAT2ATP1B2: 7,646,627–7,657,771, forward strandATP1B2TP53: 7,661,779–7,687,546, reverse strandTP53WRAP53: 7,686,071–7,703,505, forward strandWRAP53EFNB3: 7,705,172–7,711,372, forward strandEFNB3DNAH2: 7,717,728–7,833,742, forward strandDNAH2KDM6B: 7,834,217–7,854,796, forward strandKDM6BTMEM88: 7,855,057–7,856,114, forward strandTMEM88NAA38: 7,856,681–7,885,238, reverse strandNAA38CYB5D1: 7,857,696–7,862,282, forward strandCYB5D1CHD3: 7,884,787–7,912,760, forward strandCHD3RNF227: 7,913,238–7,916,377, reverse strandKCNAB3: 7,920,956–7,929,856, reverse strandKCNAB3: 7,925,931–7,930,622, reverse strandTRAPPC1: 7,930,345–7,932,123, reverse strandCNTROB: 7,932,101–7,949,953, forward strandCNTROBGUCY2D: 8,002,615–8,020,342, forward strandGUCY2DALOX15B: 8,039,011–8,049,134, forward strandALOX15BALOX12B: 8,068,594–8,087,716, reverse strandALOX12BALOXE3: 8,095,900–8,119,047, reverse strandALOXE3HES7: 8,120,592–8,124,114, reverse strandHES7PER1: 8,140,467–8,156,506, reverse strandPER1: 8,150,816–8,162,975, reverse strandVAMP2: 8,159,149–8,163,584, reverse strandVAMP2TMEM107: 8,172,440–8,176,408, reverse strandTMEM107BORCS6: 8,188,345–8,190,180, reverse strandAURKB: 8,204,335–8,210,638, reverse strandAURKBCTC1: 8,224,815–8,248,075, reverse strandCTC1PFAS: 8,247,618–8,271,150, forward strandPFASSLC25A35: 8,287,762–8,295,410, reverse strandSLC25A35RANGRF: 8,288,631–8,290,092, forward strandRANGRFARHGEF15: 8,310,222–8,323,203, forward strandARHGEF15ODF4: 8,339,840–8,346,048, forward strandODF4Diagram of KDM6B: 24 exons on the forward strand of chromosome 17Exon 5: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 9: 2 known disease-causing sitesExon 11: 5 known disease-causing sitesExon 12: 10 known disease-causing sitesExon 13: 1 known disease-causing siteExon 15: 1 known disease-causing siteExon 18: 1 known disease-causing siteExon 19: 3 known disease-causing sitesExon 20: 3 known disease-causing sitesExon 21: 7 known disease-causing sitesExon 1: 7,834,217–7,834,350, 134 basesExon 2: 7,839,906–7,840,024, 119 basesExon 3: 7,844,901–7,845,020, 120 basesExon 4: 7,845,314–7,845,456, 143 basesExon 5: 7,845,550–7,845,691, 142 basesExon 6: 7,845,872–7,845,970, 99 basesExon 7: 7,846,078–7,846,297, 220 basesExon 8: 7,846,400–7,846,492, 93 basesExon 9: 7,846,579–7,846,740, 162 basesExon 10: 7,846,819–7,847,016, 198 basesExon 11: 7,847,105–7,847,452, 348 basesExon 12: 7,847,546–7,849,728, 2,183 basesExon 13: 7,849,821–7,849,947, 127 basesExon 14: 7,850,072–7,850,177, 106 basesExon 15: 7,851,021–7,851,226, 206 basesExon 16: 7,851,330–7,851,394, 65 basesExon 17: 7,851,478–7,851,549, 72 basesExon 18: 7,851,648–7,851,796, 149 basesExon 19: 7,851,951–7,852,065, 115 basesExon 20: 7,852,149–7,852,336, 188 basesExon 21: 7,852,495–7,852,636, 142 basesExon 22: 7,853,000–7,853,126, 127 basesExon 23: 7,853,210–7,853,380, 171 basesExon 24: 7,853,498–7,854,796, 1,299 bases15101520245′3′

    Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

    Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

    Nearby genes from Ensembl release 116, on GRCh38.

    Exons make up 6.7 kb of the gene's 20.6 kb; 4,932 of those bases code for the protein.

    How a genome test reads KDM6B

    42

    positions in KDM6B where ClinVar classes a change as pathogenic or likely pathogenic

    None of them falls in a region short reads find hard.

    A whole genome covers all 20.6 kb of KDM6B, introns included, not only the 6.7 kb of exons.

    Where this comes from

    • HGNC: the gene's symbol, name, other symbols and location.
    • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
    • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
    • The ACMG secondary findings list, SF v3.2.
    • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
    • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
    • Data release 2026.10.16-c6eea6bf.

    Cite this page

    APA

    Dante Labs. (n.d.). KDM6B gene: lysine demethylase 6B. Retrieved 17 October 2026, from https://dantelabs.com/genes/kdm6b

    Vancouver

    Dante Labs. KDM6B gene: lysine demethylase 6B [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/kdm6b

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