Gene

HNF1A

HNF1 homeobox A

Cytogenetic location: 12q24.31
Coordinates: Chromosome 12: 120,978,543–121,002,512 (GRCh38)
Exons: 10 exons across 24 kb
Protein: 631 amino acids
Inheritance: Autosomal dominant
Also known as: HNF1, LFB1, HNF1α
Previous symbols: MODY3, TCF1
MANE Select transcript: ENST00000257555.11NM_000545.8
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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Curated reports relevant to this gene

Diabetes Mellitus
- A metabolic disorder characterized by abnormally high blood sugar levels due to diminished production of insulin or insulin resistance/desensitization.
  - ClinGen rates the link definitive
  - 4 GenCC submitters rate it definitive or strong
  - On the ACMG secondary findings list
  What knowing changes
  Teplizumab (Tzield) for stage 2 presymptomatic T1D (FDA approved 2022); insulin replacement at clinical T1D onset; TrialNet autoantibody screening for high-risk relatives; closed-loop insulin delivery systems
Maturity-Onset Diabetes Of The Young
- Autosomal dominant
  MODY (maturity-onset diabetes of the young) is a rare, familial, clinically and genetically heterogeneous form of diabetes characterized by young age of onset (generally 10-45 years of age) with maintenance of endogenous insulin production, lack of pancreatic beta-cell autoimmunity, absence of obesity and insulin resistance and extra-pancreatic manifestations in some subtypes.
  - 3 GenCC submitters rate it definitive or strong
  - On the ACMG secondary findings list
  What knowing changes
  GCK-MODY: no treatment needed; HNF1A/HNF4A-MODY: low-dose sulfonylureas; HNF1B-MODY: insulin + renal monitoring; T2D polygenic: lifestyle modification, metformin, GLP-1 agonists, SGLT2 inhibitors based on comorbidity profile

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.

How a genome test reads HNF1A

246

positions in HNF1A 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 24 kb of HNF1A, introns included, not only the 3.4 kb of exons.

Variants with a page (245)

The HNF1A variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

Variant	HGVS c.	Exon or intron	Position (GRCh38)	ClinVar classification	Review status
A15Gfs*15	c.42_51delinsTG	Exon 1	120,978,810	Pathogenic	3 stars out of 4 reviewed by expert panel
A116T	c.346G>A	Exon 2	120,988,852	Likely pathogenic	3 stars out of 4 reviewed by expert panel
A116V	c.347C>T	Exon 2	120,988,853	Pathogenic	3 stars out of 4 reviewed by expert panel
A209E	c.626C>A	Exon 3	120,993,619	Likely pathogenic	3 stars out of 4 reviewed by expert panel
A209Sfs*11	c.620dup	Exon 3	120,993,609	Pathogenic	3 stars out of 4 reviewed by expert panel
A239T	c.715G>A	Exon 4	120,994,165	Likely pathogenic	3 stars out of 4 reviewed by expert panel
A276D	c.827C>A	Exon 4	120,994,277	Pathogenic	3 stars out of 4 reviewed by expert panel
A276G	c.827C>G	Exon 4	120,994,277	Likely pathogenic	3 stars out of 4 reviewed by expert panel
A406V	c.1217C>T	Exon 6	120,996,650	Likely pathogenic	3 stars out of 4 reviewed by expert panel
A501T	c.1501G>A	Exon 7	120,997,665	Pathogenic	3 stars out of 4 reviewed by expert panel

See all 245 HNF1A variants →

Traits linked to HNF1A

The Human Phenotype Ontology lists these as features of the rare conditions HNF1A can cause. Each trait's page lists the other genes linked to it.

Laboratory abnormality

Show 17 more traits

Abnormality of the nervous system

Abnormality of the genitourinary system

Growth abnormality

Abnormality of the digestive system

Abnormality of the cardiovascular system

Abnormality of the endocrine system

Abnormality of the integument

Abnormality of the immune system

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 2026-10-16: 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

APA

Dante Labs. (n.d.). HNF1A gene: HNF1 homeobox A. Retrieved 16 October 2026, from https://dantelabs.com/genes/hnf1a

Vancouver

Dante Labs. HNF1A gene: HNF1 homeobox A [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/hnf1a

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