HERPUD1

homocysteine inducible ER protein with ubiquitin like domain 1

Basic information

Region (hg38): 16:56932142-56944864

Links

ENSG00000051108 ∙ NCBI:9709 ∙ OMIM:608070 ∙ HGNC:13744 ∙ Uniprot:Q15011 ∙ 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 HERPUD1 gene.

• Hereditary breast ovarian cancer syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HERPUD1 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	2		7
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	5	2	0

Variants in HERPUD1

This is a list of pathogenic ClinVar variants found in the HERPUD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-56932266-G-A		not specified	Uncertain significance (Jan 23, 2023)
16-56935458-C-T		not specified	Uncertain significance (Mar 30, 2024)
16-56935470-G-A		not specified	Likely benign (Oct 04, 2022)
16-56936702-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-56939282-C-G		not specified	Uncertain significance (Nov 14, 2023)
16-56939290-A-G		not specified	Uncertain significance (May 30, 2024)
16-56939358-T-C		not specified	Uncertain significance (May 14, 2024)
16-56939921-CTT-C		Hereditary breast ovarian cancer syndrome	Pathogenic (Aug 01, 2020)
16-56940008-A-C		not specified	Uncertain significance (May 13, 2024)
16-56942138-C-A		not specified	Uncertain significance (Dec 18, 2023)
16-56942167-C-T		not specified	Likely benign (Dec 08, 2023)
16-56942206-T-G		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HERPUD1	protein_coding	protein_coding	ENST00000439977	8	11839

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00418	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.800	187	220	0.848	0.0000112	2556
Missense in Polyphen		38	67.144	0.56595		854
Synonymous	0.417	77	81.8	0.941	0.00000435	767
Loss of Function	4.00	1	20.6	0.0486	0.00000105	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins. Could enhance presenilin-mediated amyloid-beta protein 40 generation. Binds to ubiquilins and this interaction is required for efficient degradation of CD3D via the ERAD pathway (PubMed:18307982). {ECO:0000269|PubMed:16289116, ECO:0000269|PubMed:18307982}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);ATF4 activates genes;VEGFA-VEGFR2 Signaling Pathway;Exercise-induced Circadian Regulation (Consensus)

Recessive Scores

• pRec: 0.285

Intolerance Scores

• loftool: 0.761
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.0647
• hipred: Y
• hipred_score: 0.775
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.928

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Herpud1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;response to unfolded protein;retrograde protein transport, ER to cytosol;regulation of protein ubiquitination;positive regulation of protein binding;endoplasmic reticulum calcium ion homeostasis;response to endoplasmic reticulum stress;PERK-mediated unfolded protein response;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway;positive regulation of ER-associated ubiquitin-dependent protein catabolic process;negative regulation of intrinsic apoptotic signaling pathway
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;membrane;calcium channel complex;Lewy body core
• Molecular function: molecular_function;protein binding;ion channel binding