HDGF

heparin binding growth factor, the group of Heparin binding growth factor family

Basic information

Region (hg38): 1:156742108-156766925

Links

ENSG00000143321 ∙ NCBI:3068 ∙ OMIM:600339 ∙ HGNC:4856 ∙ Uniprot:P51858 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDGF 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in HDGF

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

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

Position	Type	Phenotype	Significance	ClinVar
1-156743659-G-A		not specified	Uncertain significance (Nov 09, 2022)
1-156743722-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-156743733-T-C		not specified	Uncertain significance (Sep 26, 2023)
1-156743745-C-T		not specified	Uncertain significance (Apr 07, 2023)
1-156743746-G-A		not specified	Uncertain significance (Jun 27, 2022)
1-156743797-G-A		not specified	Uncertain significance (Dec 15, 2023)
1-156743799-G-C		not specified	Uncertain significance (Jul 12, 2023)
1-156744168-G-T		not specified	Uncertain significance (Apr 23, 2024)
1-156744234-C-A		not specified	Uncertain significance (Apr 25, 2022)
1-156744285-C-G		not specified	Uncertain significance (May 30, 2024)
1-156744329-C-G		not specified	Uncertain significance (Sep 29, 2023)
1-156744339-T-G		not specified	Uncertain significance (Mar 15, 2024)
1-156745012-T-C		not specified	Uncertain significance (Jul 13, 2021)
1-156745061-C-T		not specified	Uncertain significance (Jan 08, 2024)
1-156745332-G-T		not specified	Uncertain significance (Aug 02, 2021)
1-156752232-A-T		not specified	Likely benign (Sep 28, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDGF	protein_coding	protein_coding	ENST00000368206	6	24819

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.273	0.723	125738	0	8	125746	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	102	144	0.707	0.00000765	1689
Missense in Polyphen		25	55.027	0.45432		682
Synonymous	0.115	57	58.1	0.981	0.00000384	471
Loss of Function	2.44	3	12.2	0.246	6.16e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000277	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000236	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Heparin-binding protein, with mitogenic activity for fibroblasts. Acts as a transcriptional repressor. {ECO:0000269|PubMed:17974029}.
• Pathway: XBP1(S) activates chaperone genes (Consensus)

Intolerance Scores

• loftool: 0.627
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.668
• hipred: N
• hipred_score: 0.210
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hdgf
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;signal transduction;cell population proliferation;regulation of signaling receptor activity;IRE1-mediated unfolded protein response;cellular response to interleukin-7
• Cellular component: extracellular region;extracellular space;nucleoplasm;cytoplasm;transcriptional repressor complex;collagen-containing extracellular matrix
• Molecular function: nucleotide binding;transcription corepressor binding;DNA binding;transcription corepressor activity;RNA binding;growth factor activity;heparin binding