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Gene

CRLF1

cytokine receptor like factor 1

Summary

Cytogenetic location
19p12
Coordinates
Chromosome 19: 18,593,237–18,606,799 (GRCh38)
Exons
9 exons across 13.6 kb
Protein
422 amino acids
Also known as
CLF-1, CLF, CISS, CISS1
MANE Select transcript
ENST00000392386.8NM_004750.5
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

  • Hereditary Sensory and Autonomic Neuropathies (incl. Familial Dysautonomia)

    • Hereditary Sensory and Autonomic Neuropathy

      A group of neuropathies, including familial dysautonomia (ELP1), HSAN1 (SPTLC1/SPTLC2), HSAN2 (WNK1, RETREG1) and congenital insensitivity to pain (NTRK1, SCN9A, PRDM12), most of which are recessive while HSAN1 is dominant.

      • 3 GenCC submitters rate it definitive or strong
      What knowing changes

      Protection against unnoticed injuries, burns and infections, management of autonomic symptoms, and carrier testing for relatives (familial dysautonomia is included in Ashkenazi Jewish carrier screening).

How CRLF1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 19, with a bracket where CRLF1 sits. CRLF1 and 36 genes near it on chromosome 19, from 18,100,018 to 19,100,017.Chromosome 1919p12p13.3p13.2p13.13p13.12p13.11p12p11q11q12q13.11q13.12q13.13q13.2q13.31q13.32q13.33q13.41q13.42q13.4318.2 Mb18.4 Mb18.6 Mb18.8 Mb19 MbMAST3: 18,097,749–18,151,692, forward strandMAST3PIK3R2: 18,153,155–18,170,541, forward strandPIK3R2: 18,153,158–18,178,117, forward strandIFI30: 18,173,150–18,178,122, forward strandIFI30MPV17L2: 18,193,197–18,196,948, forward strandRAB3A: 18,196,752–18,204,055, reverse strandRAB3APDE4C: 18,207,961–18,255,419, reverse strandPDE4CPDE4C: 18,207,965–18,248,200, reverse strandPDE4CCIST1: 18,249,950–18,255,400, reverse strandCIST1IQCN: 18,257,098–18,274,500, reverse strandIQCNJUND: 18,279,694–18,281,622, reverse strandJUNDLSM4: 18,306,231–18,323,112, reverse strandLSM4PGPEP1: 18,340,562–18,369,950, forward strandPGPEP1GDF15: 18,374,731–18,389,176, forward strandGDF15LRRC25: 18,390,351–18,397,622, reverse strandLRRC25SSBP4: 18,418,864–18,434,563, forward strandSSBP4ISYNA1: 18,434,388–18,438,309, reverse strandISYNA1ELL: 18,442,663–18,522,116, reverse strandELLFKBP8: 18,531,751–18,544,264, reverse strandFKBP8KXD1: 18,557,683–18,569,387, forward strandUBA52: 18,571,722–18,577,550, forward strandUBA52REX1BD: 18,588,685–18,592,342, forward strandREX1BDCRLF1: 18,593,237–18,606,799, reverse strandCRLF1TMEM59L: 18,607,335–18,621,050, forward strandTMEM59LKLHL26: 18,637,018–18,671,721, forward strandKLHL26CRTC1: 18,683,575–18,782,333, forward strandCRTC1COMP: 18,782,773–18,791,312, reverse strandCOMPUPF1: 18,831,905–18,868,232, forward strandUPF1GDF1: 18,868,545–18,896,158, reverse strandGDF1CERS1: 18,868,545–18,896,727, reverse strandCERS1COPE: 18,899,511–18,919,407, reverse strandCOPE: 18,907,013–18,934,397, reverse strandDDX49: 18,919,667–18,929,189, forward strandHOMER3: 18,929,201–18,941,728, reverse strandSUGP2: 18,990,887–19,061,647, reverse strandSUGP2ARMC6: 19,033,575–19,060,311, forward strandARMC6SLC25A42: 19,061,697–19,113,030, forward strandSLC25A42Diagram of CRLF1: 9 exons on the reverse strand of chromosome 19Exon 6: 2 known disease-causing sitesExon 5: 6 known disease-causing sitesExon 4: 4 known disease-causing sitesExon 1: 4 known disease-causing sitesExon 9: 18,593,237–18,593,579, 343 basesExon 8: 18,594,065–18,594,107, 43 basesExon 7: 18,594,247–18,594,434, 188 basesExon 6: 18,596,622–18,596,790, 169 basesExon 5: 18,596,892–18,597,049, 158 basesExon 4: 18,598,432–18,598,601, 170 basesExon 3: 18,598,772–18,598,901, 130 basesExon 2: 18,599,565–18,599,846, 282 basesExon 1: 18,606,542–18,606,799, 258 bases9876543215′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 1.7 kb of the gene's 13.6 kb; 1,269 of those bases code for the protein.

How a genome test reads CRLF1

19

positions in CRLF1 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 13.6 kb of CRLF1, introns included, not only the 1.7 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.). CRLF1 gene: cytokine receptor like factor 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/crlf1

Vancouver

Dante Labs. CRLF1 gene: cytokine receptor like factor 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/crlf1

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