HERPUD2

HERPUD family member 2

Basic information

Region (hg38): 7:35632659-35697459

Links

ENSG00000122557 ∙ NCBI:64224 ∙ ∙ HGNC:21915 ∙ Uniprot:Q9BSE4 ∙ 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 HERPUD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HERPUD2 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			21
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	0	0

Variants in HERPUD2

This is a list of pathogenic ClinVar variants found in the HERPUD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-35633791-T-C		not specified	Uncertain significance (Sep 16, 2021)
7-35633848-G-A		not specified	Uncertain significance (Mar 31, 2023)
7-35634382-T-C		not specified	Uncertain significance (Apr 15, 2022)
7-35635166-T-C		not specified	Uncertain significance (Oct 29, 2021)
7-35635216-G-A		not specified	Uncertain significance (Apr 07, 2023)
7-35635256-G-C		not specified	Uncertain significance (Mar 21, 2024)
7-35635274-T-C		not specified	Uncertain significance (Dec 13, 2023)
7-35635394-G-T		not specified	Uncertain significance (Oct 12, 2022)
7-35635453-G-C		not specified	Uncertain significance (Jun 09, 2022)
7-35638404-G-A		not specified	Uncertain significance (Apr 26, 2024)
7-35638414-C-T		not specified	Uncertain significance (Mar 31, 2023)
7-35667453-A-G		not specified	Uncertain significance (Feb 10, 2022)
7-35667498-G-A		not specified	Uncertain significance (Nov 09, 2022)
7-35667500-T-C		not specified	Uncertain significance (Mar 12, 2024)
7-35670231-G-C		not specified	Uncertain significance (Jan 09, 2024)
7-35670253-T-C		not specified	Uncertain significance (May 02, 2024)
7-35670259-T-G		not specified	Uncertain significance (Aug 05, 2023)
7-35670283-G-A		not specified	Uncertain significance (Dec 13, 2023)
7-35673233-C-T		not specified	Uncertain significance (Nov 03, 2023)
7-35694215-G-A		not specified	Uncertain significance (Oct 05, 2023)
7-35694311-T-G		not specified	Uncertain significance (Sep 13, 2023)
7-35694314-A-G		not specified	Uncertain significance (Aug 08, 2023)
7-35694315-T-A		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HERPUD2	protein_coding	protein_coding	ENST00000396081	8	62913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.947	0.0530	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	176	220	0.799	0.0000109	2668
Missense in Polyphen		36	63.599	0.56604		778
Synonymous	-0.124	81	79.6	1.02	0.00000414	779
Loss of Function	3.81	3	22.5	0.133	0.00000120	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000582	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000582	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could be involved in the unfolded protein response (UPR) pathway. {ECO:0000250}.

Intolerance Scores

• loftool: 0.345
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.304
• hipred: Y
• hipred_score: 0.644
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.175

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Herpud2

Gene ontology

• Biological process: response to unfolded protein;spermatogenesis
• Cellular component: integral component of membrane