HEPN1

hepatocellular carcinoma, down-regulated 1

Basic information

Region (hg38): 11:124919249-124920677

Links

ENSG00000221932 ∙ NCBI:641654 ∙ OMIM:611641 ∙ HGNC:34400 ∙ Uniprot:Q6WQI6 ∙ 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 HEPN1 gene.

• Megalencephalic leukoencephalopathy with subcortical cysts (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEPN1 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			1			1
missense					2	2
nonsense			1			1
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	2

Variants in HEPN1

This is a list of pathogenic ClinVar variants found in the HEPN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-124919286-G-A		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 12, 2018)
11-124919286-G-C		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 12, 2018)
11-124919336-A-AAAAC		Megalencephalic leukoencephalopathy with subcortical cysts	Benign (Jun 14, 2016)
11-124919339-A-G		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 13, 2018)
11-124919504-T-C		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 12, 2018)
11-124919524-T-A		Megalencephalic leukoencephalopathy with subcortical cysts	Benign (Jan 12, 2018)
11-124919659-A-G		Megalencephalic leukoencephalopathy with subcortical cysts	Likely benign (Jan 13, 2018)
11-124919662-G-A		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 13, 2018)
11-124919686-AG-A		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jun 14, 2016)
11-124919846-AAGG-A		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jun 14, 2016)
11-124919859-T-C		Megalencephalic leukoencephalopathy with subcortical cysts	Benign (Jan 13, 2018)
11-124919860-G-A		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 12, 2018)
11-124919903-C-T		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 12, 2018)
11-124919932-A-T		Megalencephalic leukoencephalopathy with subcortical cysts	Benign (Jan 13, 2018)
11-124920105-T-C		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 13, 2018)
11-124920114-C-G		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 13, 2018)
11-124920149-C-A		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 13, 2018)
11-124920195-C-T		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Apr 27, 2017)
11-124920276-G-T		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 12, 2018)
11-124920307-C-A		Megalencephalic leukoencephalopathy with subcortical cysts	Likely benign (Jan 12, 2018)
11-124920411-C-T		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 12, 2018)
11-124920429-G-A		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 13, 2018)
11-124920472-C-T		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jan 12, 2018)
11-124920509-C-T		Megalencephalic leukoencephalopathy with subcortical cysts	Uncertain significance (Jun 14, 2016)
11-124920666-A-C		Megalencephalic leukoencephalopathy with subcortical cysts	Likely benign (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HEPN1	protein_coding	protein_coding	ENST00000408930	1	1428

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.147	45	47.9	0.940	0.00000243	569
Missense in Polyphen		10	10.032	0.99681		129
Synonymous	-0.492	22	19.3	1.14	9.14e-7	176
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.674
• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.81

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Cellular component: cytoplasm