HAND1
protein-codingheart and neural crest derivatives expressed 1, the group of Basic helix-loop-helix proteins
Gene summary
The protein encoded by this gene belongs to the basic helix-loop-helix family of transcription factors. This gene product is one of two closely related family members, the HAND proteins, which are asymmetrically expressed in the developing ventricular chambers and play an essential role in cardiac morphogenesis. Working in a complementary fashion, they function in the formation of the right ventricle and aortic arch arteries, implicating them as mediators of congenital heart disease. In addition, it has been suggested that this transcription factor may be required for early trophoblast differentiation. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0005453
Submitter: ClinGen
*HAND1* was first reported in relation to autosomal dominant congenital heart disease in 2012 (Cheng et al., PMID 22032825). At least 3 rare variants (2 missense, 1 frameshift) have been reported in humans. Additional, more frequent missense variants have been reported in blood (Wang et al., PMID 21519287; Cheng et al., PMID: 22032825) and fixed tissue (Reamon-Buettner et al., PMID 18276607; Reamon-Buettner et al., PMID 19586923). Evidence supporting this gene-disease relationship includes case-level data and experimental data. *HAND1* has been noted to be associated with the following disease entities: double-outlet right ventricle with ventricular septal defect, tetralogy of Fallot, and ventricular septal defect (OMIM 602406). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found no difference in molecular mechanism and inheritance pattern. Therefore, these disease entities have been lumped into one disease entity, autosomal dominant *HAND1*-related Congenital Heart Defects. Of note, this gene has also been implicated in abnormalities of placental development and function. These will be assessed separately. Variants in this gene have been reported in at least 3 probands in 3 publications (PMIDs 28112363, 27942761, 22032825), using an allele frequency threshold of 1x10-5. This gene-disease relationship is supported by animal models, expression studies, and functional assays. Expression studies confirmed that *HAND1* is expressed early in mouse and human embryogenesis (PMIDs 7649392, 36563664, 25050861, 28521042, 31341279, 30759401). Loss of *HAND1* resulted in abnormal cardioid formation from human induced pluripotent stem cells (PMIDs 34446706, 34019794). Mouse models demonstrated that cardiac-specific insufficiency and overexpression of *HAND1* both altered cardiac development, particularly the differentiation of ventricular cardiomyocytes (PMIDs 33757801, 17050624, 31286141). In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged. This classification was approved by the ClinGen Congenital Heart Disease GCEP on the meeting date 04/3/23 (SOP Version 9).
Inheritance Pattern: AD
Disease ID:MONDO:0005453
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HAND1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004821.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 50 | 1 | 51 | |||
| missense | 114 | 7 | 121 | |||
| nonsense | 2 | 2 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 120 | 57 | 1 | 178 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004812.1 | 2 | MANE Select | |
| Ensembl | ENSP00000231121.2 | 2 | MANE Select | |
| Ensembl | ENSP00000548352.1 | 2 | Standard | |
| Ensembl | ENSP00000786982.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human)
- Heart Development
- Neural Crest Differentiation
- Mesodermal Commitment Pathway
- nfat and hypertrophy of the heart
Biological Process
- negative regulation of transcription by RNA polymerase II
- angiogenesis
- mesoderm formation
- blastocyst development
- trophectodermal cell differentiation
Molecular Function
- RNA polymerase II proximal promoter sequence-specific DNA binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA-binding transcription repressor activity, RNA polymerase II-specific
- transcription coactivator activity
- protein binding
Cellular Component
- nucleus
- nucleoplasm
- nucleolus
- cytoplasm
- RNA polymerase II transcription factor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000231121
- Coding exons
- 2
- Length
- 3293
- Individuals with no LoFs
- 125691
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125694
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.284 | 133 | 124 | 1.07 | 0.00000587 | 1377 |
| Missense (PolyPhen) | 34 | 36.396 | 0.93416 | 428 | ||
| Synonymous | -1.18 | 64 | 53.1 | 1.21 | 0.00000271 | 449 |
| Loss of Function | 1.27 | 2 | 5.09 | 0.393 | 2.19e-7 | 66 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transcription factor that plays an essential role in both trophoblast-giant cells differentiation and in cardiac morphogenesis. In the adult, could be required for ongoing expression of cardiac-specific genes. Binds the DNA sequence 5'- NRTCTG-3' (non-canonical E-box) (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.230
Intolerance Scores
- LoFtool
- 0.216
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 56.64
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.994
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |