H19

H19 imprinted maternally expressed transcript, the group of MicroRNA non-coding host genes|Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 11:1995165-2004552

Links

ENSG00000130600 ∙ NCBI:283120 ∙ OMIM:103280 ∙ HGNC:4713 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Beckwith-Wiedemann syndrome (Strong), mode of inheritance: AD
• Beckwith-Wiedemann syndrome (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Wilms tumor 2; Beckwith-Wiedemann syndrome	AD (with imprinting)	Endocrine; Oncologic	Surveillance for and early diagnosis of Wilms tumor could be beneficial in order to allow early treatment, which could benefit related morbidity and mortality; Recognition and surveillance for and treatment of neonatal hypoglycemia can be beneficial	Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Oncologic; Renal	15314640; 15743916; 18836444
The causes involve imprinting effects

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the H19 gene.

• Beckwith-Wiedemann syndrome (8 variants)
• not provided (4 variants)
• H19-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H19 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	4	0	0

Variants in H19

This is a list of pathogenic ClinVar variants found in the H19 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-1995427-C-T		H19-related disorder	Likely benign (Apr 24, 2019)
11-1995437-C-T		H19-related disorder	Likely benign (Jul 06, 2022)
11-1995476-T-A			Uncertain significance (Mar 28, 2021)
11-1995487-T-A		H19-related disorder	Benign (Mar 30, 2019)
11-1995514-A-G		H19-related disorder	Likely benign (Aug 21, 2019)
11-1995543-A-T		H19-related disorder	Likely benign (Jul 13, 2024)
11-1995748-GGT-G			Uncertain significance (Oct 01, 2023)
11-1996115-C-A		H19-related disorder	Likely benign (Mar 21, 2019)
11-1996127-G-A		H19-related disorder	Likely benign (Jun 15, 2019)
11-1996133-G-A		H19-related disorder	Likely benign (Mar 20, 2019)
11-1996177-C-T			Benign (Apr 01, 2024)
11-1996191-T-C		H19-related disorder	Likely benign (Jul 13, 2019)
11-1996297-G-A		H19-related disorder	Likely benign (Jun 19, 2019)
11-1996431-G-A		H19-related disorder	Likely benign (May 01, 2019)
11-1996507-GA-G		H19-related disorder	Likely benign (Jun 10, 2020)
11-1996532-C-T			Benign (Jan 01, 2024)
11-1996553-C-T		H19-related disorder	Likely benign (Jun 11, 2020)
11-1996629-C-T		H19-related disorder	Likely benign (Feb 21, 2019)
11-1996665-A-G		H19-related disorder	Benign (Mar 20, 2019)
11-1996772-C-T		MIR675-related disorder	Likely benign (Dec 17, 2019)
11-1996914-G-A		H19-related disorder	Likely benign (May 25, 2019)
11-1996956-C-T		H19-related disorder	Likely benign (Mar 30, 2019)
11-1996989-C-G		H19-related disorder	Likely benign (Apr 17, 2024)
11-1997058-G-A		H19-related disorder	Likely benign (Feb 22, 2019)
11-1997095-T-C		H19-related disorder	Likely benign (Oct 22, 2019)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Pathway: H19 action Rb-E2F1 signaling and CDK-β-catenin activity (Consensus)

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.231