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Gene

PCYT1A

phosphate cytidylyltransferase 1A, choline

Summary

Cytogenetic location
3q29
Coordinates
Chromosome 3: 196,234,368–196,287,726 (GRCh38)
Exons
9 exons across 53.4 kb
Protein
367 amino acids
Also known as
CT, CTPCT, CCTalpha
Previous symbols
PCYT1
MANE Select transcript
ENST00000431016.6NM_001312673.2
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 reports relevant to this gene

No Genome Test report reads PCYT1A yet. The test sequences your whole genome, so your data includes it all the same.

How PCYT1A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 3, with a bracket where PCYT1A sits. PCYT1A and 19 genes near it on chromosome 3, from 195,761,047 to 196,761,046.Chromosome 33q29p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q29195.8 Mb196 Mb196.2 Mb196.4 Mb196.6 MbMUC4: 195,746,765–195,811,973, reverse strandMUC4TNK2: 195,863,364–195,911,945, reverse strandTNK2: 195,908,695–195,909,561, reverse strandTFRC: 196,012,511–196,082,162, reverse strandTFRCZDHHC19: 196,197,452–196,211,437, reverse strandZDHHC19SLC51A: 196,211,487–196,244,766, forward strandSLC51APCYT1A: 196,234,368–196,287,726, reverse strandPCYT1A: 196,248,230–196,318,222, reverse strandDYNLT2B: 196,291,219–196,318,328, reverse strandDYNLT2BTM4SF19-DYNLT2B: 196,316,082–196,338,373, reverse strandTM4SF19-DYNLT2BTM4SF19: 196,319,342–196,338,604, reverse strandTM4SF19UBXN7: 196,347,659–196,432,476, reverse strandUBXN7RNF168: 196,468,783–196,503,824, reverse strandRNF168SMCO1: 196,506,877–196,515,368, reverse strandSMCO1WDR53: 196,552,217–196,569,263, reverse strandWDR53FBXO45: 196,568,611–196,589,059, forward strandFBXO45NRROS: 196,639,676–196,707,522, forward strandNRROSPIGX: 196,639,775–196,736,016, forward strandPIGXCEP19: 196,706,268–196,712,603, reverse strandCEP19PAK2: 196,739,743–196,832,647, forward strandPAK2Diagram of PCYT1A: 9 exons on the reverse strand of chromosome 3Exon 9: 1 known disease-causing siteExon 8: 3 known disease-causing sitesExon 7: 2 known disease-causing sitesExon 5: 3 known disease-causing sitesExon 4: 3 known disease-causing sitesExon 9: 196,234,368–196,238,894, 4,527 basesExon 8: 196,239,547–196,239,735, 189 basesExon 7: 196,241,948–196,242,090, 143 basesExon 6: 196,242,562–196,242,640, 79 basesExon 5: 196,247,367–196,247,518, 152 basesExon 4: 196,248,207–196,248,323, 117 basesExon 3: 196,257,788–196,257,887, 100 basesExon 2: 196,270,415–196,270,541, 127 basesExon 1: 196,287,615–196,287,726, 112 bases9864215′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 5.5 kb of the gene's 53.4 kb; 1,104 of those bases code for the protein.

How a genome test reads PCYT1A

15

positions in PCYT1A 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 53.4 kb of PCYT1A, introns included, not only the 5.5 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.
  • 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.). PCYT1A gene: phosphate cytidylyltransferase 1A, choline. Retrieved 17 October 2026, from https://dantelabs.com/genes/pcyt1a

Vancouver

Dante Labs. PCYT1A gene: phosphate cytidylyltransferase 1A, choline [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/pcyt1a

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