HSPBAP1

HSPB1 associated protein 1, the group of Iron (II) and 2-oxoglutarate dependent oxygenases

Basic information

Region (hg38): 3:122739999-122793831

Links

ENSG00000169087 ∙ NCBI:79663 ∙ OMIM:608263 ∙ HGNC:16389 ∙ Uniprot:Q96EW2 ∙ 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 HSPBAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSPBAP1 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			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	31	3	0

Variants in HSPBAP1

This is a list of pathogenic ClinVar variants found in the HSPBAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-122740405-C-A		not specified	Uncertain significance (Mar 03, 2025)
3-122740557-C-A		not specified	Uncertain significance (Jun 05, 2024)
3-122740590-C-G		not specified	Uncertain significance (Dec 20, 2023)
3-122740607-G-A		not specified	Uncertain significance (Mar 23, 2022)
3-122740646-C-A		not specified	Uncertain significance (Feb 06, 2025)
3-122740731-C-G		not specified	Uncertain significance (Mar 07, 2025)
3-122740748-T-G		not specified	Uncertain significance (Dec 28, 2022)
3-122740752-T-C		not specified	Uncertain significance (Apr 04, 2023)
3-122740769-C-G		not specified	Uncertain significance (Jul 13, 2022)
3-122740793-T-C		not specified	Uncertain significance (Sep 07, 2022)
3-122740808-C-T		not specified	Likely benign (Nov 07, 2022)
3-122740832-G-T		not specified	Uncertain significance (Jan 26, 2025)
3-122740842-A-G		not specified	Uncertain significance (Sep 03, 2024)
3-122740875-C-T		not specified	Uncertain significance (Nov 21, 2022)
3-122741065-C-G		not specified	Uncertain significance (Aug 20, 2024)
3-122741073-C-T		not specified	Uncertain significance (Nov 15, 2024)
3-122741074-G-A		not specified	Uncertain significance (Nov 21, 2022)
3-122741094-C-T		not specified	Uncertain significance (Sep 12, 2023)
3-122755313-A-G		not specified	Uncertain significance (Aug 15, 2023)
3-122755330-T-C		not specified	Uncertain significance (Dec 11, 2024)
3-122755339-T-A		not specified	Uncertain significance (Aug 10, 2021)
3-122755431-C-T		not specified	Likely benign (Jul 19, 2023)
3-122759278-G-A		not specified	Uncertain significance (Oct 03, 2022)
3-122759293-G-A		not specified	Uncertain significance (Oct 13, 2023)
3-122759296-C-A		not specified	Uncertain significance (Jan 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSPBAP1	protein_coding	protein_coding	ENST00000306103	8	53826

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.41e-11	0.339	125680	0	68	125748	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	199	258	0.770	0.0000131	3233
Missense in Polyphen		63	87.125	0.7231		1129
Synonymous	0.592	86	93.3	0.922	0.00000507	902
Loss of Function	1.02	19	24.5	0.777	0.00000132	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00139	0.00139
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in cellular stress response. {ECO:0000250}.

Recessive Scores

• pRec: 0.0863

Intolerance Scores

• loftool: 0.790
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.2

Haploinsufficiency Scores

• pHI: 0.0723
• hipred: N
• hipred_score: 0.144
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.873

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hspbap1

Gene ontology

• Cellular component: cytoplasm
• Molecular function: protein binding;2-oxoglutarate-dependent dioxygenase activity