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Gene

NIPBL

NIPBL cohesin loading factor

Summary

Cytogenetic location
5p13.2
Coordinates
Chromosome 5: 36,876,769–37,066,413 (GRCh38)
Exons
47 exons across 189.6 kb
Protein
2,804 amino acids
Also known as
IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2
MANE Select transcript
ENST00000282516.13NM_133433.4
Locus type
gene with protein product

Reference genomeGRCh38

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

Curated report relevant to this gene

  • Cornelia de Lange Syndrome

    • A developmental disorder caused by variants in NIPBL, SMC1A, SMC3, RAD21, HDAC8 or BRD4, with a wide range of severity.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Diagnosis guides monitoring for associated problems such as reflux, heart defects, hearing and vision issues.

How NIPBL 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 NIPBL sits. NIPBL and 4 genes near it on chromosome 5, from 36,471,591 to 37,471,590.Chromosome 55p13.2p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.336.6 Mb36.8 Mb37 Mb37.2 Mb37.4 MbSLC1A3: 36,596,584–36,688,335, forward strandSLC1A3NIPBL: 36,876,769–37,066,413, forward strandNIPBLCPLANE1: 37,105,973–37,249,410, reverse strandCPLANE1NUP155: 37,288,042–37,371,187, reverse strandNUP155WDR70: 37,379,244–37,753,534, forward strandWDR70Diagram of NIPBL: 47 exons on the forward strand of chromosome 5Exon 2: 7 known disease-causing sitesExon 3: 12 known disease-causing sitesExon 4: 8 known disease-causing sitesExon 5: 4 known disease-causing sitesExon 6: 4 known disease-causing sitesExon 7: 2 known disease-causing sitesExon 8: 3 known disease-causing sitesExon 9: 26 known disease-causing sitesExon 10: 65 known disease-causing sitesExon 11: 6 known disease-causing sitesExon 12: 15 known disease-causing sitesExon 13: 3 known disease-causing sitesExon 14: 1 known disease-causing siteExon 15: 4 known disease-causing sitesExon 16: 4 known disease-causing sitesExon 17: 8 known disease-causing sitesExon 18: 3 known disease-causing sitesExon 19: 4 known disease-causing sitesExon 20: 4 known disease-causing sitesExon 21: 9 known disease-causing sitesExon 22: 6 known disease-causing sitesExon 23: 8 known disease-causing sitesExon 24: 5 known disease-causing sitesExon 25: 3 known disease-causing sitesExon 26: 8 known disease-causing sitesExon 27: 4 known disease-causing sitesExon 28: 5 known disease-causing sitesExon 29: 13 known disease-causing sitesExon 30: 5 known disease-causing sitesExon 31: 5 known disease-causing sitesExon 33: 3 known disease-causing sitesExon 34: 5 known disease-causing sitesExon 35: 5 known disease-causing sitesExon 36: 7 known disease-causing sitesExon 37: 6 known disease-causing sitesExon 38: 4 known disease-causing sitesExon 39: 13 known disease-causing sitesExon 40: 11 known disease-causing sitesExon 41: 4 known disease-causing sitesExon 42: 12 known disease-causing sitesExon 43: 9 known disease-causing sitesExon 44: 8 known disease-causing sitesExon 45: 16 known disease-causing sitesExon 46: 6 known disease-causing sitesExon 47: 15 known disease-causing sitesExon 1: 36,876,769–36,877,178, 410 basesExon 2: 36,953,618–36,953,760, 143 basesExon 3: 36,955,472–36,955,637, 166 basesExon 4: 36,958,104–36,958,231, 128 basesExon 5: 36,961,484–36,961,583, 100 basesExon 6: 36,962,123–36,962,274, 152 basesExon 7: 36,970,876–36,971,036, 161 basesExon 8: 36,971,945–36,972,041, 97 basesExon 9: 36,975,776–36,976,402, 627 basesExon 10: 36,984,676–36,986,301, 1,626 basesExon 11: 36,995,622–36,995,804, 183 basesExon 12: 37,000,373–37,000,570, 198 basesExon 13: 37,000,817–37,000,888, 72 basesExon 14: 37,000,989–37,001,078, 90 basesExon 15: 37,002,662–37,002,765, 104 basesExon 16: 37,003,261–37,003,347, 87 basesExon 17: 37,006,357–37,006,588, 232 basesExon 18: 37,007,323–37,007,474, 152 basesExon 19: 37,008,008–37,008,088, 81 basesExon 20: 37,008,623–37,008,723, 101 basesExon 21: 37,010,087–37,010,225, 139 basesExon 22: 37,014,683–37,014,765, 83 basesExon 23: 37,016,038–37,016,170, 133 basesExon 24: 37,017,019–37,017,162, 144 basesExon 25: 37,019,311–37,019,400, 90 basesExon 26: 37,020,459–37,020,673, 215 basesExon 27: 37,020,775–37,020,877, 103 basesExon 28: 37,022,051–37,022,149, 99 basesExon 29: 37,022,244–37,022,390, 147 basesExon 30: 37,024,585–37,024,719, 135 basesExon 31: 37,026,229–37,026,327, 99 basesExon 32: 37,027,359–37,027,412, 54 basesExon 33: 37,036,379–37,036,487, 109 basesExon 34: 37,038,602–37,038,738, 137 basesExon 35: 37,044,347–37,044,487, 141 basesExon 36: 37,044,636–37,044,729, 94 basesExon 37: 37,045,443–37,045,597, 155 basesExon 38: 37,046,109–37,046,199, 91 basesExon 39: 37,048,502–37,048,675, 174 basesExon 40: 37,049,111–37,049,301, 191 basesExon 41: 37,051,779–37,051,886, 108 basesExon 42: 37,052,366–37,052,566, 201 basesExon 43: 37,057,186–37,057,332, 147 basesExon 44: 37,058,891–37,059,165, 275 basesExon 45: 37,060,844–37,061,018, 175 basesExon 46: 37,063,790–37,063,978, 189 basesExon 47: 37,064,527–37,066,413, 1,887 bases151015202530354045475′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 10.4 kb of the gene's 189.6 kb; 8,415 of those bases code for the protein.

How a genome test reads NIPBL

450

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

2 of them (0.4%) fall in regions short reads find hard.

  • Segmental duplications (2 sites)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 189.6 kb of NIPBL, introns included, not only the 10.4 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.). NIPBL gene: NIPBL cohesin loading factor. Retrieved 17 October 2026, from https://dantelabs.com/genes/nipbl

Vancouver

Dante Labs. NIPBL gene: NIPBL cohesin loading factor [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/nipbl

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