HSF2BP

heat shock transcription factor 2 binding protein, the group of Armadillo like helical domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 21:43529186-43659488

Links

ENSG00000160207 ∙ NCBI:11077 ∙ OMIM:604554 ∙ HGNC:5226 ∙ Uniprot:O75031 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• premature ovarian failure 19 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Premature ovarian failure 19	AR	Obstetric	The condition can involve infertility, and fertility treatment has been described as successful in some indviduals	Obstetric	32845237

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HSF2BP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSF2BP 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		2	16	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	2	17	3	0

Variants in HSF2BP

This is a list of pathogenic ClinVar variants found in the HSF2BP region.

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

Position	Type	Phenotype	Significance	ClinVar
21-43529816-G-A		not specified	Uncertain significance (Dec 18, 2023)
21-43529824-C-T		not specified	Uncertain significance (Oct 09, 2024)
21-43529848-C-T		not specified	Uncertain significance (Mar 22, 2023)
21-43529903-G-C		not specified	Uncertain significance (Sep 29, 2023)
21-43529903-G-T		not specified	Uncertain significance (Jul 20, 2022)
21-43529960-G-C		not specified	Uncertain significance (Aug 17, 2022)
21-43592280-C-T			Likely benign (Feb 01, 2024)
21-43613833-T-C		not specified	Uncertain significance (Nov 24, 2024)
21-43613852-C-A			Uncertain significance (Sep 01, 2024)
21-43613858-T-C		not specified	Uncertain significance (Nov 21, 2024)
21-43613876-GCAATATGGTGTC-G			Uncertain significance (Feb 01, 2024)
21-43613890-A-C		not specified	Uncertain significance (Oct 20, 2024)
21-43613900-G-A		not specified	Uncertain significance (Dec 12, 2022)
21-43613913-C-G		not specified	Uncertain significance (Jun 28, 2022)
21-43613923-C-T		not specified	Uncertain significance (Oct 10, 2023)
21-43630339-A-G		Premature ovarian failure 19	Likely pathogenic (Aug 01, 2021)
21-43630379-G-T		not specified	Likely benign (Dec 22, 2023)
21-43630396-G-A		Premature ovarian failure 19	Uncertain significance (Apr 04, 2024)
21-43630403-C-T		not specified	Uncertain significance (Aug 04, 2024)
21-43630413-C-T		not specified	Uncertain significance (Nov 10, 2024)
21-43630424-C-T		not specified	Uncertain significance (Jun 28, 2022)
21-43630448-C-A		not specified	Uncertain significance (Nov 13, 2023)
21-43630452-A-T		not specified	Uncertain significance (Jul 15, 2021)
21-43633273-C-T		not specified	Uncertain significance (Jun 18, 2024)
21-43633331-A-G		Premature ovarian failure 19	Likely pathogenic (Aug 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSF2BP	protein_coding	protein_coding	ENST00000291560	8	130303

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.53e-16	0.00121	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.172	197	190	1.03	0.0000112	2178
Missense in Polyphen		95	102.59	0.92603		1203
Synonymous	0.274	71	74.0	0.960	0.00000440	644
Loss of Function	-1.14	21	16.1	1.31	7.38e-7	207

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00200	0.00199
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.000109	0.000109
South Asian	0.000329	0.000327
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in modulating HSF2 activation in testis (PubMed:9651507). Inhibits BNC1 transcriptional activity during spermatogenesis, probably by sequestering it in the cytoplasm (By similarity). {ECO:0000250|UniProtKB:Q9D4G2, ECO:0000269|PubMed:9651507}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.516
• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.143
• hipred: N
• hipred_score: 0.396
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.967

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hsf2bp
• Phenotype: hematopoietic system phenotype; reproductive system phenotype; limbs/digits/tail phenotype; renal/urinary system phenotype; immune system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: transcription by RNA polymerase II;spermatogenesis
• Cellular component: cytosol
• Molecular function: protein binding