# How many genes are in a chromosome?

> A human chromosome carries about 800 protein-coding genes on average, from 61 on the Y chromosome to 2,016 on chromosome 1. See current counts for chromosomes 1 through 22, X, Y, and mitochondrial DNA.

A human chromosome carries **about 800 protein-coding genes** on average, but the spread around that average is wide. Chromosome 1 holds 2,016, roughly one in ten of all human protein-coding genes, while the Y chromosome holds 61. These figures come from GENCODE Release 50, the current reference annotation of the human genome, and count each gene once per chromosome type.

Counting every annotated gene, including non-coding RNA genes and pseudogenes, raises the average to about 3,300 per chromosome and widens the range to 672 to 7,108. The table below gives both counts for chromosomes 1 through 22, X, Y, and mitochondrial DNA.

## How many genes does each chromosome contain?

Across the 24 distinct human nuclear chromosomes, autosomes 1 to 22 plus X and Y, GENCODE Release 50 annotates 19,429 protein-coding genes, an average of about 810 per chromosome. Most chromosomes carry between 500 and 1,300. Only chromosome 1 exceeds 2,000, and chromosomes 13, 18, 21, and Y each carry fewer than 350.

Textbook answers of about 1,000 genes per chromosome come from an older total. When the finished human genome sequence was published in 2004, the sequencing consortium put the count at 20,000 to 25,000 protein-coding genes. Dividing that range by the 23 chromosomes in one set gives roughly 870 to 1,090. The current [19,442 protein-coding genes](/guides/how-many-genes-do-humans-have), less the 13 encoded by [mitochondrial DNA](/guides/how-many-genes-in-mitochondrial-dna), give about 845 by the same division.

These are counts of gene locations, or loci, on one copy of each chromosome. A typical human cell has [46 chromosomes](/guides/how-many-chromosomes-do-humans-have), two copies of each autosome, and both copies carry the same set of loci, although their DNA can differ in the versions, or alleles, of each gene. A second copy of chromosome 1 doubles the copies of its genes, not the number of distinct genes.

![Protein-coding gene counts for human chromosomes 1 through 22, X, Y, and mitochondrial DNA in GENCODE Release 50](/images/charts/human-protein-coding-genes-by-chromosome.webp '**Figure 1. Protein-coding genes on each human chromosome.** Counts exclude 665 readthrough genes, following the GENCODE headline method; M is mitochondrial DNA. Source: ProteinIQ count from [GENCODE Release 50](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_50/gencode.v50.annotation.gtf.gz).')

  <caption><strong>Table 1. Genes on each human chromosome in GENCODE Release 50.</strong> Counts are gene loci on one copy of each chromosome. We counted both columns from the gene records in the release annotation file. The protein-coding column excludes 665 readthrough genes, as the GENCODE headline total does; the second column counts every gene record, including non-coding RNA genes, pseudogenes, and immune receptor gene segments. Sources: GENCODE Release 50 annotation and statistics.</caption>
  <thead>
    <tr>
      <th scope="col">Chromosome</th>
      <th scope="col">Protein-coding genes</th>
      <th scope="col">All annotated genes</th>
    </tr>
  </thead>
  <tbody>
    <tr><td>1</td><td>2,016</td><td>7,108</td></tr>
    <tr><td>2</td><td>1,221</td><td>5,687</td></tr>
    <tr><td>3</td><td>1,041</td><td>4,159</td></tr>
    <tr><td>4</td><td>745</td><td>3,577</td></tr>
    <tr><td>5</td><td>874</td><td>3,948</td></tr>
    <tr><td>6</td><td>1,013</td><td>4,232</td></tr>
    <tr><td>7</td><td>899</td><td>3,958</td></tr>
    <tr><td>8</td><td>687</td><td>3,265</td></tr>
    <tr><td>9</td><td>754</td><td>3,188</td></tr>
    <tr><td>10</td><td>713</td><td>3,271</td></tr>
    <tr><td>11</td><td>1,282</td><td>4,171</td></tr>
    <tr><td>12</td><td>1,004</td><td>3,862</td></tr>
    <tr><td>13</td><td>315</td><td>2,000</td></tr>
    <tr><td>14</td><td>595</td><td>2,795</td></tr>
    <tr><td>15</td><td>571</td><td>2,819</td></tr>
    <tr><td>16</td><td>822</td><td>3,186</td></tr>
    <tr><td>17</td><td>1,140</td><td>3,793</td></tr>
    <tr><td>18</td><td>260</td><td>1,652</td></tr>
    <tr><td>19</td><td>1,393</td><td>3,543</td></tr>
    <tr><td>20</td><td>526</td><td>1,972</td></tr>
    <tr><td>21</td><td>216</td><td>1,133</td></tr>
    <tr><td>22</td><td>428</td><td>1,747</td></tr>
    <tr><td>X</td><td>853</td><td>2,958</td></tr>
    <tr><td>Y</td><td>61</td><td>672</td></tr>
    <tr><td>Mitochondrial DNA</td><td>13</td><td>37</td></tr>
  </tbody>

Chromosome size is a poor guide to gene count, because genes are not spread evenly along the genome. Chromosome 19 carries 1,393 protein-coding genes, more than chromosome 2's 1,221, although chromosome 2 contains far more [DNA](/guides/how-long-is-dna).

When the finished sequence of chromosome 19 was published in 2004, Grimwood and colleagues found the highest gene density of any human chromosome, more than double the genome-wide average, with nearly a quarter of its genes in tandem families of related genes.

## Why do chromosome gene counts differ between sources?

Chromosome gene counts differ because sources count different kinds of genes, and because annotations change as evidence accumulates.

GENCODE Release 50 contains 20,107 gene records with the protein-coding biotype. Its headline total is 19,442 because 665 readthrough genes, which join parts of two neighboring genes into one transcript, are reported separately. Counting every gene record, including long non-coding RNA genes, small RNA genes, pseudogenes, and immune receptor segments, gives 78,733.

Older figures are often higher. The annotation published with the finished sequence of chromosome 1 in 2006 reported 3,141 genes and 991 pseudogenes, which is why many reference pages still describe chromosome 1 as carrying more than 3,000 genes. Today it has 2,016 protein-coding genes, or 7,108 gene records of all types, so a figure from any source means little until you know which gene types and which release it counts.

Gene catalogs also shift because a gene has to be supported by evidence. An [ORF finder](/app/orf-finder) can locate open reading frames, stretches of DNA that could encode a protein, but annotators also weigh transcript, protein, and cross-species evidence before calling one a protein-coding gene. Candidates gain or lose that status between releases, and per-chromosome totals move with them.

## How many genes are on the X and Y chromosomes?

The human X chromosome has 853 protein-coding genes and 2,958 annotated genes of all types in GENCODE Release 50. The Y chromosome has 61 and 672. The National Human Genome Research Institute gives rounded figures of about 900 genes for X and about 55 for Y.

Under the same GENCODE method, X carries about 14 times as many protein-coding genes as Y. The gap is smaller for all gene types, about 4.4 times, because about nine in ten of the Y chromosome's 672 gene records are pseudogenes, non-coding RNA genes, or other loci that do not count as protein-coding.

![The X chromosome has 853 protein-coding genes and 2,958 annotated genes of all types, compared with 61 and 672 on the Y chromosome](/images/charts/x-y-chromosome-gene-counts.webp '**Figure 2. Gene counts on the human X and Y chromosomes.** Protein-coding counts exclude readthrough genes; all-annotated counts include every gene record. Source: ProteinIQ count from [GENCODE Release 50](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_50/gencode.v50.annotation.gtf.gz).')

## How many chromatids and centromeres are in a chromosome?

A chromosome has one chromatid before DNA replication and two sister chromatids after replication; a typical human chromosome has one centromere.

A chromatid is one replicated copy of a chromosome. After the cell copies its [genome](/guides/how-long-does-dna-replication-take), the two sister chromatids remain joined until they separate during cell division. A human cell can therefore have 46 chromosomes and 92 chromatids after replication but before the sister chromatids separate.

Each normal chromosome has one centromere, along with two telomeres and multiple origins of replication. Replication copies the centromeric DNA along with the rest of the chromosome, allowing the two sister chromatids to attach to the mitotic spindle and move into separate daughter cells.

A replicated chromosome 1 therefore carries its 2,016 protein-coding genes twice, once on each sister chromatid, and division hands one copy to each daughter cell. Replication changes how many copies of each gene a cell holds at a given moment, not how many distinct genes a chromosome carries.