Gene

MSH4

mutS homolog 4

Cytogenetic location: 1p31.1
Coordinates: Chromosome 1: 75,796,882–75,913,242 (GRCh38)
Exons: 20 exons across 116.4 kb
Protein: 936 amino acids
MANE Select transcript: ENST00000263187.4NM_002440.4
Locus type: Protein-coding

Very high
Confident
Low
Very low

This page as data

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Curated report relevant to this gene

Female Infertility
- Diminished or absent ability of a female to achieve conception.
  - 2 GenCC submitters rate it definitive or strong

How MSH4 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 3.3 kb of the gene's 116.4 kb; 2,811 of those bases code for the protein.

Sequencing MSH4

positions in MSH4 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 116.4 kb of MSH4, introns included, not only the 3.3 kb of exons.

ClinVar pathogenic variants (3)

The MSH4 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.

Pathogenic 1
Likely pathogenic 2

Variant	Conditions	ClinVar classification	Review status
NM_002440.4(MSH4):c.2261C>T (p.Ser754Leu) (opens in a new tab)	oligospermia	Pathogenic	1 star out of 4 criteria provided, single submitter
NM_002440.4(MSH4):c.232del (p.Arg78fs) (opens in a new tab)	premature ovarian failure 20 and 1 other	Likely pathogenic	1 star out of 4 criteria provided, single submitter
NM_002440.4(MSH4):c.2639_2640del (p.Pro880fs) (opens in a new tab)	premature ovarian failure 20 and 1 other	Likely pathogenic	1 star out of 4 criteria provided, single submitter

Traits linked to MSH4

The Human Phenotype Ontology lists these as features of the rare conditions MSH4 can cause. Each trait's page lists the other genes linked to it.

Abnormality of the genitourinary system

Show 5 more traits

Abnormality of the endocrine system

Abnormality of the musculoskeletal system

Abnormality of the integument

External links

Gene records

Transcript

Protein

Variants

Clinical

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 2026-10-18: 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 2026.10.18-8b139e39.

Cite this page

APA

Dante Labs. (n.d.). MSH4 gene: mutS homolog 4. Retrieved 18 October 2026, from https://dantelabs.com/genes/msh4

Vancouver

Dante Labs. MSH4 gene: mutS homolog 4 [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/msh4

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