HDGFL1

HDGF like 1, the group of Heparin binding growth factor family

Basic information

Region (hg38): 6:22569566-22571666

Previous symbols: [ "PWWP1" ]

Links

ENSG00000112273 ∙ NCBI:154150 ∙ ∙ HGNC:21095 ∙ Uniprot:Q5TGJ6 ∙ 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 HDGFL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDGFL1 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in HDGFL1

This is a list of pathogenic ClinVar variants found in the HDGFL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-22569583-C-T		not specified	Uncertain significance (Feb 27, 2023)
6-22569588-G-A		not specified	Uncertain significance (Mar 28, 2023)
6-22569640-A-G		not specified	Uncertain significance (Dec 08, 2023)
6-22569663-G-C		not specified	Uncertain significance (Jun 16, 2023)
6-22569739-G-A		not specified	Likely benign (Dec 21, 2022)
6-22569784-A-G		not specified	Uncertain significance (Jan 09, 2024)
6-22569850-A-G		not specified	Uncertain significance (Jun 13, 2022)
6-22569855-C-T		not specified	Uncertain significance (Sep 26, 2023)
6-22569861-G-A		not specified	Uncertain significance (Jul 12, 2023)
6-22569864-T-G		not specified	Uncertain significance (Aug 30, 2022)
6-22569915-G-A		not specified	Uncertain significance (Apr 09, 2024)
6-22569931-C-T		not specified	Uncertain significance (Mar 28, 2024)
6-22569975-G-A		not specified	Uncertain significance (Mar 01, 2024)
6-22569980-C-G		not specified	Uncertain significance (Dec 02, 2022)
6-22570032-C-T		not specified	Uncertain significance (Apr 04, 2024)
6-22570053-C-T		not specified	Uncertain significance (Sep 17, 2021)
6-22570089-G-A		not specified	Uncertain significance (Apr 17, 2023)
6-22570102-C-G		not specified	Uncertain significance (Apr 18, 2023)
6-22570140-A-C		not specified	Uncertain significance (Jun 11, 2021)
6-22570149-G-T		not specified	Uncertain significance (Sep 06, 2022)
6-22570167-C-T		not specified	Uncertain significance (Dec 16, 2023)
6-22570188-A-C		not specified	Uncertain significance (Jan 17, 2024)
6-22570244-G-C		not specified	Uncertain significance (Jun 12, 2023)
6-22570263-G-A		not specified	Uncertain significance (May 29, 2024)
6-22570267-A-G		not specified	Uncertain significance (Aug 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDGFL1	protein_coding	protein_coding	ENST00000510882	1	2215

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0587	0.874	125702	0	11	125713	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.450	149	165	0.902	0.0000125	1617
Missense in Polyphen		27	48.792	0.55336		476
Synonymous	0.177	84	86.1	0.976	0.00000846	469
Loss of Function	1.54	3	7.56	0.397	4.04e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000307	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.238
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0706

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hdgfl1