PHB2

prohibitin 2

Basic information

Region (hg38): 12:6965327-6970780

Links

ENSG00000215021 ∙ NCBI:11331 ∙ OMIM:610704 ∙ HGNC:30306 ∙ Uniprot:Q99623 ∙ 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 PHB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHB2 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	13	0	3

Variants in PHB2

This is a list of pathogenic ClinVar variants found in the PHB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-6965706-G-A			Benign (Mar 29, 2018)
12-6965713-CTG-C			Benign (Jun 02, 2018)
12-6966468-T-C			Benign (Jun 02, 2018)
12-6966469-G-T		not specified	Uncertain significance (Sep 17, 2021)
12-6966475-T-C		not specified	Uncertain significance (Feb 12, 2024)
12-6967172-G-A		not specified	Uncertain significance (Oct 26, 2024)
12-6967702-C-T		not specified	Uncertain significance (Oct 17, 2023)
12-6967713-A-G		not specified	Uncertain significance (Mar 14, 2023)
12-6967927-C-T		not specified	Uncertain significance (Oct 26, 2022)
12-6967964-G-C		not specified	Uncertain significance (Oct 17, 2023)
12-6968487-G-A		not specified	Uncertain significance (Nov 09, 2021)
12-6968520-C-T		not specified	Uncertain significance (Apr 06, 2023)
12-6968550-T-C		not specified	Uncertain significance (May 09, 2023)
12-6969572-G-A		not specified	Uncertain significance (Nov 06, 2023)
12-6970229-T-C		not specified	Uncertain significance (Nov 08, 2021)
12-6970429-A-G		not specified	Uncertain significance (Dec 21, 2022)
12-6970430-T-A		not specified	Uncertain significance (Sep 26, 2024)
12-6970446-G-A		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHB2	protein_coding	protein_coding	ENST00000535923	10	5499

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00393	0.995	124481	3	201	124685	0.000818

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	102	176	0.579	0.0000100	1910
Missense in Polyphen		25	67.874	0.36833		735
Synonymous	0.960	60	70.2	0.854	0.00000357	608
Loss of Function	2.77	8	22.0	0.363	0.00000142	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00697	0.00685
Ashkenazi Jewish	0.00119	0.00119
East Asian	0.00235	0.00223
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000180	0.000177
Middle Eastern	0.00235	0.00223
South Asian	0.000232	0.000229
Other	0.000999	0.000990

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a mediator of transcriptional repression by nuclear hormone receptors via recruitment of histone deacetylases (By similarity). Functions as an estrogen receptor (ER)-selective coregulator that potentiates the inhibitory activities of antiestrogens and represses the activity of estrogens. Competes with NCOA1 for modulation of ER transcriptional activity. Probably involved in regulating mitochondrial respiration activity and in aging. {ECO:0000250|UniProtKB:O35129, ECO:0000269|PubMed:10359819, ECO:0000303|PubMed:11302691}.
• Pathway: Transport of small molecules;Mitochondrial calcium ion transport;Validated nuclear estrogen receptor alpha network;Processing of SMDT1 (Consensus)

Intolerance Scores

• loftool: 0.523
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.409
• hipred: Y
• hipred_score: 0.756
• ghis: 0.561

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phb2
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; reproductive system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: obsolete protein import into nucleus, translocation;mitochondrial calcium ion transmembrane transport;mitochondrion organization;sister chromatid cohesion;regulation of complement activation;positive regulation of exit from mitosis;negative regulation of intracellular estrogen receptor signaling pathway;negative regulation of mammary gland epithelial cell proliferation;negative regulation of apoptotic process;negative regulation of DNA-binding transcription factor activity;negative regulation of transcription, DNA-templated;protein stabilization;positive regulation of DNA-binding transcription factor activity;mammary gland branching involved in thelarche;mammary gland alveolus development;regulation of branching involved in mammary gland duct morphogenesis;positive regulation of ERK1 and ERK2 cascade;positive regulation of cell cycle G1/S phase transition
• Cellular component: nucleus;cytoplasm;mitochondrion;mitochondrial outer membrane;mitochondrial inner membrane;cell surface;nuclear matrix;protein-containing complex;cell periphery
• Molecular function: protein binding;protein C-terminus binding;estrogen receptor binding;amide binding;protein N-terminus binding