HS1BP3

HCLS1 binding protein 3

Basic information

Region (hg38): 2:20560448-20651130

Links

ENSG00000118960 ∙ NCBI:64342 ∙ OMIM:609359 ∙ HGNC:24979 ∙ Uniprot:Q53T59 ∙ 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 HS1BP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HS1BP3 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				2		2
missense			32	4	1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	6	1

Variants in HS1BP3

This is a list of pathogenic ClinVar variants found in the HS1BP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-20619033-A-G		not specified	Uncertain significance (May 23, 2023)
2-20619041-C-A		not specified	Uncertain significance (Apr 12, 2023)
2-20619052-T-A		not specified	Uncertain significance (Feb 22, 2023)
2-20619056-G-A			Likely benign (Oct 01, 2023)
2-20619122-G-T			Likely benign (Feb 01, 2023)
2-20619241-C-T		not specified	Uncertain significance (Aug 28, 2023)
2-20623916-G-T		not specified	Likely benign (May 09, 2023)
2-20623935-G-A		not specified	Uncertain significance (Oct 17, 2023)
2-20623954-C-T		not specified	Uncertain significance (Dec 06, 2022)
2-20623960-C-T		not specified	Uncertain significance (Apr 25, 2022)
2-20623965-G-A		not specified	Uncertain significance (Oct 20, 2021)
2-20623986-A-G		not specified	Uncertain significance (Dec 27, 2023)
2-20624002-C-T		not specified	Uncertain significance (May 10, 2023)
2-20624818-T-C		not specified	Uncertain significance (Dec 20, 2023)
2-20624819-C-T		not specified	Uncertain significance (Feb 06, 2024)
2-20624842-G-A			Likely benign (Mar 01, 2023)
2-20624845-G-A		not specified	Conflicting classifications of pathogenicity (Jul 01, 2024)
2-20624853-T-G		not specified	Uncertain significance (Dec 17, 2021)
2-20624881-G-T		not specified	Uncertain significance (Oct 26, 2022)
2-20638491-C-T		not specified	Uncertain significance (May 01, 2022)
2-20638517-G-A		not specified	Likely benign (Jul 13, 2021)
2-20641021-A-T		not specified	Uncertain significance (Jun 11, 2021)
2-20641029-C-T		not specified	Uncertain significance (Feb 07, 2023)
2-20641063-G-A			Benign (Jul 01, 2023)
2-20641066-T-A		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HS1BP3	protein_coding	protein_coding	ENST00000304031	7	90642

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000119	0.595	125680	0	66	125746	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.186	223	231	0.966	0.0000134	2541
Missense in Polyphen		78	76.447	1.0203		919
Synonymous	-0.0398	102	101	1.00	0.00000671	795
Loss of Function	0.949	11	15.0	0.735	8.03e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000580	0.000577
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000224	0.000220
Middle Eastern	0.000435	0.000435
South Asian	0.000561	0.000555
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a modulator of IL-2 signaling. {ECO:0000250}.

Recessive Scores

• pRec: 0.0992

Intolerance Scores

• loftool: 0.787
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.73

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.216
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.118

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hs1bp3

Zebrafish Information Network

• Gene name: hs1bp3
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: negative regulation of autophagy;regulation of apoptotic process
• Cellular component: mitochondrion;endoplasmic reticulum
• Molecular function: protein binding;phosphatidylinositol binding