HDGFL2

HDGF like 2, the group of Heparin binding growth factor family

Basic information

Region (hg38): 19:4472297-4502208

Links

ENSG00000167674 ∙ NCBI:84717 ∙ OMIM:617884 ∙ HGNC:14680 ∙ Uniprot:Q7Z4V5 ∙ 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 HDGFL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDGFL2 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			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	0

Variants in HDGFL2

This is a list of pathogenic ClinVar variants found in the HDGFL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4493812-C-T		not specified	Uncertain significance (Aug 04, 2021)
19-4493993-C-T		not specified	Uncertain significance (Aug 30, 2021)
19-4494212-G-A		not specified	Uncertain significance (Nov 09, 2021)
19-4497974-C-T		not specified	Uncertain significance (Jun 11, 2021)
19-4499498-G-A		not specified	Uncertain significance (Sep 16, 2021)
19-4499600-A-G			Likely benign (Jan 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDGFL2	protein_coding	protein_coding	ENST00000301284	16	29940

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.775	0.225	124780	0	7	124787	0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	301	399	0.754	0.0000284	4322
Missense in Polyphen		17	21.743	0.78186		199
Synonymous	0.317	176	181	0.970	0.0000146	1307
Loss of Function	4.19	6	31.3	0.192	0.00000174	402

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000194	0.000194
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000184	0.0000177
Middle Eastern	0.000111	0.000111
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in cellular growth control, through the regulation of cyclin D1 expression. {ECO:0000269|PubMed:25689719}.

Haploinsufficiency Scores

• ghis: 0.519

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Hdgfl2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: positive regulation of cell growth
• Cellular component: nucleus
• Molecular function: protein binding