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Hearing loss

Gene: HGF

Amber List (moderate evidence)

HGF (hepatocyte growth factor)
EnsemblGeneIds (GRCh38): ENSG00000019991
EnsemblGeneIds (GRCh37): ENSG00000019991
OMIM: 142409, Gene2Phenotype
HGF is in 2 panels

5 reviews

Eleanor Williams (Genomics England Curator)

Comment on list classification: After review with the GMS hearing specialist test group in a Webex on 2019-02-13 and consultation with the Genomics England clinical team it was decided to rate this gene Amber and add a watchlist tag.
Created: 12 Jun 2019, 11:38 a.m.
Associated with Deafness, autosomal recessive 39 (#608265) in OMIM

PMID: 19576567 - Schultz et al 2009 - in consanguineous Pakistani and Indian families with autosomal recessive profound prelingual deafness they identified 3 homozygous mutations in the HGF gene. One is a synonymous substitution (S165S) in exon 5 and a 3-bp (1986TGA) and a 10-bp deletion (NT482+1991) in intron 4. The synonymous substitution was shown to affect splicing in vitro, and the 2 deletions occur in a highly conserved sequence that is part of the 3-prime untranslated region of a previously undescribed short isoform of HGF.

PMID: 27610647 Chen et al 2016 - no access to publication and HGF not mentioned in abstract.

PMID: 30303587 - Richard et al 2019 - consanguineous Pakistani families they found the same two deletion variants reported by Shultz et al 2009. Homozygous c.482+1986_1988del was found in 26 consanguineous Pakistani families - likely founder mutation. c.482+1991_2000del - found in 1 other family.
Created: 5 Jun 2019, 11:04 a.m.

Emma Ashton (Great Ormond Street Hospital)

I don't know

Schultz et al 2009 PMID 19576567 report two intronic deletions and a silent splice variant associated with DFNB39. Potential regulatory mutations. One other report since Chen et al 2016 PMID 27610647. Further report Richard et al 2019 PMID 30303587 26 consanguineous Pakistani families homozygous c.482+1986_1988del - described as a founder mutation in this population (originally reported by Schultz et al 2009) and 1 family homozygous for another of the variants reported by Schulz et al c.482+1991_2000del.
Created: 17 Feb 2019, 4:35 p.m.

Publications

Ellen McDonagh (Genomics England Curator)

Comment on list classification: This is currently a confirmed DD gene for deafness autosomal recessive type 39, and mutant alleles of HGF were reported to segregate with hearing loss in four different families in PMID: 19576567. However, as it is difficult to interpret variants within this gene, this was discussed internally and with members of the DDD G2P team, and it was decided that the gene should be demoted to red.
Created: 2 Mar 2016, 6:30 p.m.
Comment on mode of pathogenicity: PMID: 19576567 reports a synonymous mutation that is prediccted to affect splicing, a 3bp deletion in intron 4 predicted and a 10bp deletion in intron 4. Mutation consequence on G2P is loss of function.
Created: 17 Feb 2016, 4:19 p.m.
Comment on mode of inheritance: Confirmed on G2P and OMIM.
Created: 17 Feb 2016, 4:02 p.m.

Jun Shen (Harvard Medical School)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
#608265:Deafness, autosomal recessive 39[Deafness, sensorineural, prelingual, profoundNonprogressive deafness]

Maria Bitner-Glindzicz (UCL)

I don't know

Very few mutations described. two are intronic and affect the 3'UTR of one transcript; another synonymous change affects splicing.
Created: 30 Sep 2015, 2:46 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Mode of pathogenicity
Other

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Expert
  • Radboud University Medical Center, Nijmegen
  • Emory Genetics Laboratory
  • UKGTN
  • Illumina TruGenome Clinical Sequencing Services
Phenotypes
  • Nonsyndromic Hearing Loss, Mixed
  • Deafness, autosomal recessive 39, 608265
Tags
watchlist
OMIM
142409
Clinvar variants
Variants in HGF
Penetrance
Complete
Publications
Mode of Pathogenicity
Other - please provide details in the comments
Panels with this gene

History Filter Activity

12 Jun 2019, Gel status: 2

Added Tag

Eleanor Williams (Genomics England Curator)

Tag watchlist tag was added to gene: HGF.

12 Jun 2019, Gel status: 2

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: hgf has been classified as Amber List (Moderate Evidence).

1 May 2019, Gel status: 1

Set publications

Eleanor Williams (Genomics England Curator)

Publications for gene: HGF were set to PMID:11343646; 11564764; 11565020; 12574630; 1386343; 14556002; 14691191; 1531136; 1535333; 15545993; 17467663; 1824873; 1831266; 1837534; 19188684; 19576567; 2142751; 21988987; 21988988; 22763439; 22763448; 2528952; 2531289; 3276728; 7624797; 7854452; 7854453; 8804995; 8898205

2 Mar 2016, Gel status: 1

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

2 Mar 2016, Gel status: 2

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

17 Feb 2016, Gel status: 4

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

17 Feb 2016, Gel status: 4

Set Phenotypes

Ellen McDonagh (Genomics England Curator)

Phenotypes for HGF were set to Nonsyndromic Hearing Loss, Mixed; Deafness, autosomal recessive 39, 608265

17 Feb 2016, Gel status: 4

Set publications

Ellen McDonagh (Genomics England Curator)

Publications for HGF were set to PMID:11343646; 11564764; 11565020; 12574630; 1386343; 14556002; 14691191; 1531136; 1535333; 15545993; 17467663; 1824873; 1831266; 1837534; 19188684; 19576567; 2142751; 21988987; 21988988; 22763439; 22763448; 2528952; 2531289; 3276728; 7624797; 7854452; 7854453; 8804995; 8898205

17 Feb 2016, Gel status: 4

Set mode of pathogenicity

Ellen McDonagh (Genomics England Curator)

Mode of pathogenicity for HGF was changed to Other - please provide details in the comments

17 Feb 2016, Gel status: 4

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

17 Feb 2016, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Mode of inheritance for HGF was changed to BIALLELIC, autosomal or pseudoautosomal

24 Jun 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene HGF was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

24 Jun 2015, Gel status: 4

Added New Source

Ellen McDonagh (Genomics England Curator)

HGF was added to Congenital hearing impairment (Profound/Severe)panel. Sources: Illumina TruGenome Clinical Sequencing Services,UKGTN,Emory Genetics Laboratory,Radboud University Medical Center, Nijmegen,Expert

24 Jun 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene HGF was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

24 Jun 2015, Gel status: 4

Added New Source

Ellen McDonagh (Genomics England Curator)

HGF was added to Congenital hearing impairment (Profound/Severe)panel. Sources: Illumina TruGenome Clinical Sequencing Services,UKGTN,Emory Genetics Laboratory,Radboud University Medical Center, Nijmegen,Expert

24 Jun 2015, Gel status: 3

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene HGF was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

24 Jun 2015, Gel status: 3

Added New Source

Ellen McDonagh (Genomics England Curator)

HGF was added to Congenital hearing impairment (Profound/Severe)panel. Sources: Illumina TruGenome Clinical Sequencing Services,UKGTN,Emory Genetics Laboratory,Radboud University Medical Center, Nijmegen,Expert

24 Jun 2015, Gel status: 2

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene HGF was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

24 Jun 2015, Gel status: 2

Added New Source

Ellen McDonagh (Genomics England Curator)

HGF was added to Congenital hearing impairment (Profound/Severe)panel. Sources: Illumina TruGenome Clinical Sequencing Services,UKGTN,Emory Genetics Laboratory,Radboud University Medical Center, Nijmegen,Expert

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

HGF was added to Congenital hearing impairment (Profound/Severe)panel. Sources: Illumina TruGenome Clinical Sequencing Services,UKGTN,Emory Genetics Laboratory,Radboud University Medical Center, Nijmegen,Expert