HDGFL3

HDGF like 3, the group of Heparin binding growth factor family

Basic information

Region (hg38): 15:83112738-83207875

Links

ENSG00000166503 ∙ NCBI:50810 ∙ OMIM:616643 ∙ HGNC:24937 ∙ Uniprot:Q9Y3E1 ∙ 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 HDGFL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDGFL3 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 HDGFL3

This is a list of pathogenic ClinVar variants found in the HDGFL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-83112799-C-A		not specified	Uncertain significance (Oct 10, 2023)
15-83112825-C-G		not specified	Uncertain significance (Sep 22, 2022)
15-83112852-G-A		not specified	Uncertain significance (Mar 21, 2024)
15-83112856-G-A		not specified	Uncertain significance (Oct 01, 2024)
15-83112864-G-A		not specified	Uncertain significance (Jan 23, 2024)
15-83112882-C-T		not specified	Uncertain significance (Feb 15, 2023)
15-83112895-T-C		not specified	Uncertain significance (Dec 12, 2023)
15-83115871-G-A		not specified	Uncertain significance (Dec 10, 2024)
15-83115887-T-C		not specified	Uncertain significance (Apr 23, 2024)
15-83119586-G-A			Likely benign (Jun 01, 2022)
15-83119649-G-A		not specified	Uncertain significance (Nov 27, 2023)
15-83119675-C-T		not specified	Uncertain significance (Dec 20, 2021)
15-83121938-T-C		not specified	Uncertain significance (May 18, 2022)
15-83122777-T-G		not specified	Uncertain significance (Nov 15, 2024)
15-83122840-T-C		not specified	Uncertain significance (Feb 06, 2024)
15-83122855-G-A		not specified	Uncertain significance (Aug 17, 2022)
15-83126795-C-T		not specified	Uncertain significance (Dec 14, 2022)
15-83127368-A-G		not specified	Uncertain significance (Jun 26, 2023)
15-83136496-A-G		not specified	Uncertain significance (Mar 08, 2024)
15-83136497-T-C		not specified	Uncertain significance (Nov 08, 2022)
15-83136521-C-T		not specified	Uncertain significance (Apr 20, 2023)
15-83136578-T-C		not specified	Uncertain significance (Nov 12, 2024)
15-83136614-G-A		not specified	Uncertain significance (Dec 14, 2021)
15-83136617-G-T		not specified	Uncertain significance (Aug 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDGFL3	protein_coding	protein_coding	ENST00000299633	6	92451

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.974	0.0262	125703	0	2	125705	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	57	102	0.561	0.00000514	1323
Missense in Polyphen		16	25.042	0.63891		327
Synonymous	1.46	26	37.4	0.696	0.00000199	357
Loss of Function	3.10	0	11.2	0.00	5.68e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhances DNA synthesis and may play a role in cell proliferation. {ECO:0000269|PubMed:10581169}.

Haploinsufficiency Scores

• ghis: 0.640

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Hdgfl3

Gene ontology

• Biological process: negative regulation of microtubule depolymerization;cell population proliferation;regulation of signaling receptor activity;neuron projection development;microtubule polymerization
• Cellular component: extracellular region;nucleus;nucleoplasm;cytosol
• Molecular function: microtubule binding;growth factor activity;tubulin binding