AtlasGene
PCNT
pericentrin
- HGNC 16068↗(opens in a new tab)
- Ensembl gene ENSG00000160299↗(opens in a new tab)
- NCBI Gene 5116↗(opens in a new tab)
Summary
- Cytogenetic location
- 21q22.3
- Coordinates
- Chromosome 21: 46,324,156–46,445,769 (GRCh38)
- Exons
- 47 exons across 121.6 kb
- Protein
- 3,336 amino acids
- Also known as
- KEN, KIAA0402, PCN, PCNTB, SCKL4
- Previous symbols
- PCNT2
- MANE Select transcript
- ENST00000359568.10NM_006031.6
- Locus type
- Protein-coding
AtlasThis page as data
Add .json to the page's address, or ask for application/json, to read it as JSON.
library(jsonlite)
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No Genome Test report reads PCNT yet. The test sequences your whole genome, so your data includes it all the same.
How PCNT is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
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 10.5 kb of the gene's 121.6 kb; 10,011 of those bases code for the protein.
Sequencing PCNT
4Low
How hard PCNT is to sequence with short reads, out of 100Each bar is the share of PCNT's exon bases in that kind of difficult region. The score weighs them by how much each costs a short-read call: 0 when no base is in any, 100 when every base is in all of them.
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. Weight 35%.1.2%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 30%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 15%.5.2%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.28%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 10%.0%
124
positions in PCNT where ClinVar classes a change as pathogenic or likely pathogenic
1 of them (0.8%) falls in a region short reads find hard.
- Low mappabilityRegions where 100 bp or 250 bp reads cannot be placed uniquely. (1 site)
A whole genome covers all 121.6 kb of PCNT, introns included, not only the 10.5 kb of exons.
Traits linked to PCNT
The Human Phenotype Ontology lists these as features of the rare conditions PCNT can cause. Each trait's page lists the other genes linked to it.
Abnormality of head or neck
- Abnormally small head
- Beaked nose
- Decreased number of teeth
- Deformity of the skull
- Little lower jaw
- Narrow face
- Prominent nose
- Abnormal tooth enamel
Show 14 more traits
- Decreased size of tooth
- Downward slanting of the opening between the eyelids
- Full cheeks
- Receding chin
- Sparse or absent eyebrows
- Sparse scalp hair
- Underdeveloped tissue around nostril
- Wide nasal bridge
- Big sella turcica
- Narrow eyelid opening
- Prominent nasal bridge
- Sloping forehead
- Thin dental enamel
- Upward slanting of the opening between the eyelids
Abnormality of the nervous system
- Cognitive impairment
- High pitched voice
- Intellectual disability
- Mild global developmental delay
- Attention deficit
- Epilepsy
- Global developmental delay
- Underdevelopment of part of brain called corpus callosum
Show 1 more trait
External links
Gene records
Transcript
Protein
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 Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.17-8666dff2.
Cite this page
Dante Labs. (n.d.). PCNT gene: pericentrin. Retrieved 17 October 2026, from https://dantelabs.com/genes/pcnt
Dante Labs. PCNT gene: pericentrin [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/pcnt
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