HAND1

protein-coding

heart 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

NM_004821.3

Inheritance

AD

ClinVar variants

U:120B:58

Top phenotype

Hypoplastic left heart syndrome

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr5:154,474,972-154,478,227

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~3.3 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

congenital heart diseaseMODERATE

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).

congenital heart diseaseMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0005453

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HAND1 variants in ClinVar

4 Conditions Cataloged
Hypoplastic left heart syndromeTotal: 161
not specifiedTotal: 38
not providedTotal: 12
HAND1-related disorderTotal: 7

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.

EffectPLPVUSLBBSum
synonymous
50
clinvar
1
clinvar
51
missense
114
clinvar
7
clinvar
121
nonsense
2
clinvar
2
start loss
1
clinvar
1
frameshift
2
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total00120571178
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_004821.3RefSeqNP_004812.12MANE Select
ENST00000231121.3EnsemblENSP00000231121.22MANE Select
ENST00000878293.1EnsemblENSP00000548352.12Standard
ENST00001117177.1EnsemblENSP00000786982.12Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.2841331241.070.000005871377
Missense (PolyPhen)3436.3960.93416428
Synonymous-1.186453.11.210.00000271449
Loss of Function1.2725.090.3932.19e-766

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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