Gene
PMS2
PMS1 homolog 2, mismatch repair system component
- HGNC 9122(opens in a new tab)
- Ensembl gene ENSG00000122512(opens in a new tab)
- NCBI Gene 5395(opens in a new tab)
Summary
- Cytogenetic location
- 7p22.1
- Coordinates
- Chromosome 7: 5,970,925–6,009,049 (GRCh38)
- Exons
- 15 exons across 38.1 kb
- Protein
- 862 amino acids
- Inheritance
- Autosomal dominant Autosomal recessive
- Also known as
- H_DJ0042M02.9, HNPCC4, MLH4, PMS-2
- Previous symbols
- PMSL2
- MANE Select transcript
- ENST00000265849.12NM_000535.7
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
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DNA Repair Disease
- Autosomal recessive
A disease that has its basis in the disruption of DNA repair.
- ClinGen rates the link definitive
- 3 GenCC submitters rate it definitive or strong
Lynch Syndrome
- Autosomal dominant
Hereditary nonpolyposis colorectal cancer syndrome caused by germline mismatch-repair defects, with early-onset colorectal, endometrial and other cancers.
- ClinGen rates the link definitive
- 4 GenCC submitters rate it definitive or strong
- On the ACMG secondary findings list
What knowing changes
Enhanced colonoscopy surveillance, aspirin chemoprevention, immune checkpoint inhibitors for MSI-high tumors, cascade testing, risk-reducing gynecological surgery
Inheritance
- Autosomal dominant
- One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.
- Autosomal recessive
- It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.
How PMS2 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
- Variants with a page
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 5.1 kb of the gene's 38.1 kb; 2,589 of those bases code for the protein.
How a genome test reads PMS2
643
positions in PMS2 where ClinVar classes a change as pathogenic or likely pathogenic
483 of them (75%) fall in regions short reads find hard.
- Low mappability (273 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
- Segmental duplications (483 sites)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 38.1 kb of PMS2, introns included, not only the 5.1 kb of exons.
Variants with a page (166)
The PMS2 variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.
| Variant | Exon or intron | Position (GRCh38) | ClinVar classification | Review status |
|---|---|---|---|---|
| c.1A>G | Exon 1 | 6,009,019 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| c.24-12_107delinsAAAT | Exon 2 | 6,005,948 | Pathogenic | 3 stars out of 4 reviewed by expert panel |
| c.163+2T>C | Intron 2 | 6,005,890 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| c.164-2A>G | Intron 2 | 6,004,060 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| c.164-518_803+252delinsCG | Intron 7 | 5,997,074 | Pathogenic | 3 stars out of 4 reviewed by expert panel |
| c.251-2A>G | Intron 3 | 6,003,794 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| c.538-478_705+456del | Intron 6 | 5,998,651 | Pathogenic | 3 stars out of 4 reviewed by expert panel |
| c.705+1G>T | Intron 6 | 5,999,107 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| c.989-2A>G | Intron 9 | 5,989,957 | Likely pathogenic | 3 stars out of 4 reviewed by expert panel |
| c.989-296_1144+706del | Intron 10 | 5,989,093 | Pathogenic | 3 stars out of 4 reviewed by expert panel |
Traits linked to PMS2
The Human Phenotype Ontology lists these as features of the rare conditions PMS2 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Agenesis of corpus callosum
- Glioblastoma multiforme
- Anxiety
- Astrocytoma
- Attention deficit
- Behavioral abnormality
- Depression
- Epilepsy
Show 18 more traits
- Gray matter heterotopia
- Irritability
- Migraine
- Rise in pressure inside skull
- Abnormal gait
- Abnormal pyramidal sign
- Abnormal speech pattern
- Benign neoplasm of the central nervous system
- Cancer of early nerve cells
- Difficulty articulating speech
- Disorder of involuntary muscle movements
- Disturbed sensory perception
- Dysgraphia
- Hallucinations
- Loss of developmental milestones
- Memory impairment
- Paralysis or weakness of one side of body
- Pins and needles feeling
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.
- 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
Dante Labs. (n.d.). PMS2 gene: PMS1 homolog 2, mismatch repair system component. Retrieved 16 October 2026, from https://dantelabs.com/genes/pms2
Dante Labs. PMS2 gene: PMS1 homolog 2, mismatch repair system component [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pms2
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