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Gene

KDM3B

lysine demethylase 3B

Summary

Cytogenetic location
5q31.2
Coordinates
Chromosome 5: 138,352,685–138,437,027 (GRCh38)
Exons
24 exons across 84.3 kb
Protein
1,761 amino acids
Also known as
KIAA1082, NET22
Previous symbols
C5orf7, JMJD1B
MANE Select transcript
ENST00000314358.10NM_016604.4
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 KDM3B is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 5, with a bracket where KDM3B sits. KDM3B and 17 genes near it on chromosome 5, from 137,894,856 to 138,894,855.Chromosome 55q31.2p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.3138 Mb138.2 Mb138.4 Mb138.6 Mb138.8 MbPKD2L2: 137,887,968–137,942,747, forward strandPKD2L2FAM13B: 137,937,960–138,051,961, reverse strandFAM13BWNT8A: 138,083,990–138,092,365, forward strandWNT8ANME5: 138,114,412–138,139,443, reverse strandNME5BRD8: 138,139,770–138,178,988, reverse strandBRD8KIF20A: 138,178,715–138,188,171, forward strandKIF20ACDC23: 138,180,663–138,213,346, reverse strandCDC23GFRA3: 138,252,380–138,274,621, reverse strandGFRA3CDC25C: 138,285,251–138,338,355, reverse strandCDC25CFAM53C: 138,331,935–138,349,729, forward strandFAM53CKDM3B: 138,352,685–138,437,027, forward strandKDM3BREEP2: 138,438,976–138,446,969, forward strandREEP2EGR1: 138,465,190–138,471,204, forward strandEGR1ETF1: 138,506,093–138,543,239, reverse strandETF1HSPA9: 138,553,756–138,575,675, reverse strandHSPA9CTNNA1: 138,610,967–138,935,039, forward strandCTNNA1LRRTM2: 138,868,921–138,875,383, reverse strandLRRTM2SIL1: 138,886,914–139,293,557, reverse strandSIL1Diagram of KDM3B: 24 exons on the forward strand of chromosome 5Exon 2: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 8: 2 known disease-causing sitesExon 9: 2 known disease-causing sitesExon 10: 1 known disease-causing siteExon 11: 2 known disease-causing sitesExon 16: 2 known disease-causing sitesExon 19: 2 known disease-causing sitesExon 21: 1 known disease-causing siteExon 22: 1 known disease-causing siteExon 1: 138,352,685–138,352,987, 303 basesExon 2: 138,372,674–138,372,841, 168 basesExon 3: 138,375,093–138,375,206, 114 basesExon 4: 138,377,720–138,377,825, 106 basesExon 5: 138,379,584–138,379,708, 125 basesExon 6: 138,381,516–138,381,590, 75 basesExon 7: 138,386,022–138,386,621, 600 basesExon 8: 138,391,013–138,392,261, 1,249 basesExon 9: 138,393,171–138,393,372, 202 basesExon 10: 138,398,178–138,398,392, 215 basesExon 11: 138,399,860–138,400,012, 153 basesExon 12: 138,415,132–138,415,239, 108 basesExon 13: 138,417,483–138,417,610, 128 basesExon 14: 138,418,953–138,419,232, 280 basesExon 15: 138,420,706–138,420,962, 257 basesExon 16: 138,424,075–138,424,341, 267 basesExon 17: 138,425,411–138,425,582, 172 basesExon 18: 138,426,975–138,427,065, 91 basesExon 19: 138,427,189–138,427,319, 131 basesExon 20: 138,427,967–138,428,086, 120 basesExon 21: 138,429,826–138,429,965, 140 basesExon 22: 138,430,249–138,430,425, 177 basesExon 23: 138,431,425–138,431,559, 135 basesExon 24: 138,435,620–138,437,027, 1,408 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 84.3 kb; 5,286 of those bases code for the protein.

    How a genome test reads KDM3B

    18

    positions in KDM3B 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 84.3 kb of KDM3B, 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.). KDM3B gene: lysine demethylase 3B. Retrieved 17 October 2026, from https://dantelabs.com/genes/kdm3b

    Vancouver

    Dante Labs. KDM3B gene: lysine demethylase 3B [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/kdm3b

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