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Gene

CFC1

cryptic, EGF-CFC family member 1

Summary

Cytogenetic location
2q21.1
Coordinates
Chromosome 2: 130,592,165–130,599,575 (GRCh38)
Exons
6 exons across 7.4 kb
Protein
223 amino acids
Also known as
CRYPTIC
Previous symbols
HTX2
MANE Select transcript
ENST00000259216.6NM_032545.4
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

  • Heterotaxy & Laterality Defects

    • Visceral Heterotaxy

      Abnormal left-right arrangement of the internal organs, caused by changes in genes such as ZIC3 (X-linked), NODAL, CFC1, MMP21 and PKD1L1, often with complex heart defects and spleen abnormalities.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Knowing about it supports heart and abdominal imaging, infection precautions if the spleen is absent, and reproductive counselling.

How CFC1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where CFC1 sits. CFC1 and 16 genes near it on chromosome 2, from 130,095,870 to 131,095,869.Chromosome 22q21.1p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3130.2 Mb130.4 Mb130.6 Mb130.8 Mb131 MbPOTEF: 130,073,535–130,129,371, reverse strandPOTEFCCDC74B: 130,139,287–130,145,134, reverse strandCCDC74BSMPD4: 130,150,745–130,183,922, reverse strandSMPD4MZT2B: 130,181,737–130,190,729, forward strandMZT2BTUBA3E: 130,191,743–130,198,461, reverse strandTUBA3EVMA22: 130,337,922–130,342,699, reverse strandVMA22IMP4: 130,342,403–130,348,550, forward strandIMP4PTPN18: 130,356,026–130,375,409, forward strandPTPN18POTEI: 130,459,455–130,509,707, reverse strandPOTEICFC1B: 130,521,197–130,528,604, forward strandCFC1BCFC1: 130,592,165–130,599,575, reverse strandCFC1POTEJ: 130,611,440–130,658,037, forward strandPOTEJGPR148: 130,729,070–130,730,336, forward strandGPR148AMER3: 130,755,532–130,768,134, forward strandAMER3ARHGEF4: 130,836,864–131,047,263, forward strandARHGEF4SMIM39: 131,034,894–131,047,263, forward strandSMIM39FAM168B: 131,047,876–131,093,492, reverse strandFAM168BDiagram of CFC1: 6 exons on the reverse strand of chromosome 2Exon 3: 1 known disease-causing siteExon 6: 130,592,165–130,593,076, 912 basesExon 5: 130,597,494–130,597,603, 110 basesExon 4: 130,597,868–130,597,982, 115 basesExon 3: 130,598,642–130,598,815, 174 basesExon 2: 130,598,910–130,598,959, 50 basesExon 1: 130,599,265–130,599,575, 311 bases6543215′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 7.4 kb; 672 of those bases code for the protein.

How a genome test reads CFC1

1

position in CFC1 where ClinVar classes a change as pathogenic or likely pathogenic

1 of them (100%) falls in a region short reads find hard.

  • Low mappability (1 site)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
  • Segmental duplications (1 site)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 7.4 kb of CFC1, 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.). CFC1 gene: cryptic, EGF-CFC family member 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/cfc1

Vancouver

Dante Labs. CFC1 gene: cryptic, EGF-CFC family member 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/cfc1

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