HSF2

heat shock transcription factor 2

Basic information

Region (hg38): 6:122399551-122433119

Links

ENSG00000025156 ∙ NCBI:3298 ∙ OMIM:140581 ∙ HGNC:5225 ∙ Uniprot:Q03933 ∙ 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 HSF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSF2 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding						0
Total	0	0	25	0	0

Variants in HSF2

This is a list of pathogenic ClinVar variants found in the HSF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-122412736-A-T		not specified	Uncertain significance (May 09, 2023)
6-122413532-C-T		not specified	Uncertain significance (Jun 11, 2021)
6-122413551-T-A		not specified	Uncertain significance (Oct 02, 2023)
6-122413558-C-G		not specified	Uncertain significance (Dec 03, 2021)
6-122413559-G-A		not specified	Uncertain significance (Dec 16, 2024)
6-122413569-T-G		not specified	Uncertain significance (Feb 13, 2023)
6-122413577-A-G		not specified	Uncertain significance (Apr 22, 2022)
6-122416213-T-C			Likely benign (Oct 01, 2023)
6-122416218-TAGTG-T			Uncertain significance (Jul 10, 2019)
6-122419223-G-A		not specified	Uncertain significance (Jun 26, 2024)
6-122420187-A-G		not specified	Uncertain significance (Jan 23, 2024)
6-122420194-A-G		not specified	Uncertain significance (Jul 13, 2022)
6-122420218-A-C		not specified	Uncertain significance (Aug 07, 2024)
6-122420218-A-G		not specified	Uncertain significance (Jul 17, 2024)
6-122422157-A-G		not specified	Uncertain significance (Oct 07, 2024)
6-122422207-A-G		not specified	Uncertain significance (Mar 30, 2024)
6-122422282-A-G		not specified	Uncertain significance (Jan 10, 2025)
6-122422723-G-A		not specified	Uncertain significance (Dec 25, 2024)
6-122422759-A-G		not specified	Uncertain significance (Jun 29, 2022)
6-122422795-A-C		not specified	Uncertain significance (Sep 26, 2024)
6-122422797-C-A		not specified	Uncertain significance (Mar 01, 2024)
6-122422819-C-A		not specified	Uncertain significance (Feb 21, 2024)
6-122422846-G-A		not specified	Uncertain significance (Aug 17, 2021)
6-122422875-A-G		not specified	Uncertain significance (Dec 10, 2024)
6-122422888-G-A		not specified	Uncertain significance (Nov 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSF2	protein_coding	protein_coding	ENST00000368455	13	33574

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.975	0.0246	125728	0	11	125739	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.07	179	276	0.649	0.0000131	3578
Missense in Polyphen		41	94.323	0.43468		1346
Synonymous	-0.763	109	99.3	1.10	0.00000476	968
Loss of Function	4.30	4	29.0	0.138	0.00000149	351

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000621	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000681	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA-binding protein that specifically binds heat shock promoter elements (HSE) and activates transcription. In higher eukaryotes, HSF is unable to bind to the HSE unless the cells are heat shocked.
• Pathway: Validated nuclear estrogen receptor alpha network (Consensus)

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.115
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.33

Haploinsufficiency Scores

• pHI: 0.481
• hipred: Y
• hipred_score: 0.825
• ghis: 0.670

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hsf2
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system 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; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: transcription by RNA polymerase II;spermatogenesis;cellular response to heat;positive regulation of transcription by RNA polymerase II;positive regulation of transcription from RNA polymerase II promoter in response to heat stress
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription coactivator activity;protein binding;protein homodimerization activity;sequence-specific DNA binding