HOPX

HOP homeobox, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 4:56647989-56681877

Links

ENSG00000171476 ∙ NCBI:84525 ∙ OMIM:607275 ∙ HGNC:24961 ∙ Uniprot:Q9BPY8 ∙ 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 HOPX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOPX 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			6	2		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	8	3	2

Variants in HOPX

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

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

Position	Type	Phenotype	Significance	ClinVar
4-56648732-G-A		not specified	Benign (Jan 21, 2019)
4-56648781-C-T			Likely benign (Aug 24, 2017)
4-56650751-C-A		not specified	Likely benign (Dec 03, 2021)
4-56650792-C-G		not specified	Uncertain significance (Dec 06, 2022)
4-56650808-C-T		not specified	Uncertain significance (Sep 30, 2024)
4-56650812-C-A		not specified	Uncertain significance (Sep 25, 2023)
4-56655888-G-A			Likely benign (Aug 24, 2017)
4-56655909-G-T		not specified	Uncertain significance (Oct 07, 2024)
4-56655912-G-A		not specified	Uncertain significance (Jun 10, 2024)
4-56655924-T-C		not specified	Uncertain significance (Jun 22, 2023)
4-56655931-C-T		not specified	Uncertain significance (Jul 07, 2010)
4-56655967-C-A		not specified	Uncertain significance (Oct 18, 2021)
4-56655968-C-T		not specified	Benign (Aug 24, 2017)
4-56655975-G-C		not specified	Uncertain significance (Sep 12, 2023)
4-56655999-A-G		not specified	Uncertain significance (Oct 07, 2024)
4-56656000-T-C		not specified	Uncertain significance (Jun 11, 2024)
4-56656012-G-C		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOPX	protein_coding	protein_coding	ENST00000554144	4	33911

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000540	0.143	125713	0	11	125724	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.219	52	56.6	0.918	0.00000261	726
Missense in Polyphen		3	3.4492	0.86976		35
Synonymous	0.519	21	24.3	0.866	0.00000133	202
Loss of Function	-0.743	7	5.18	1.35	2.19e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000461	0.000431
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000334	0.0000327
Other	0.000197	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Atypical homeodomain protein which does not bind DNA and is required to modulate cardiac growth and development. Acts via its interaction with SRF, thereby modulating the expression of SRF-dependent cardiac-specific genes and cardiac development. Prevents SRF-dependent transcription either by inhibiting SRF binding to DNA or by recruiting histone deacetylase (HDAC) proteins that prevent transcription by SRF. Overexpression causes cardiac hypertrophy (By similarity). May act as a tumor suppressor. Acts as a co-chaperone for HSPA1A and HSPA1B chaperone proteins and assists in chaperone-mediated protein refolding (PubMed:27708256). {ECO:0000250|UniProtKB:Q8R1H0, ECO:0000269|PubMed:27708256}.
• Pathway: hop pathway in cardiac development (Consensus)

Recessive Scores

• pRec: 0.181

Intolerance Scores

• loftool: 0.437
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.153
• ghis: 0.646

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.310

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hopx
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; muscle 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); 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); embryo phenotype; respiratory system phenotype

Zebrafish Information Network

• Gene name: hopx
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: trophectodermal cell differentiation;regulation of transcription by RNA polymerase II;negative regulation of cell differentiation;chaperone-mediated protein complex assembly
• Cellular component: nucleus;cytoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding