HOMER3

homer scaffold protein 3, the group of Homer scaffold proteins

Basic information

Region (hg38): 19:18929201-18941261

Links

ENSG00000051128 ∙ NCBI:9454 ∙ OMIM:604800 ∙ HGNC:17514 ∙ Uniprot:Q9NSC5 ∙ 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 HOMER3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOMER3 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				1	2	3
missense			24	1		25
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	24	2	2

Variants in HOMER3

This is a list of pathogenic ClinVar variants found in the HOMER3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18929448-G-T		not specified	Uncertain significance (Feb 27, 2023)
19-18929526-C-T		not specified	Uncertain significance (May 11, 2022)
19-18929528-C-T		not specified	Uncertain significance (Dec 16, 2022)
19-18929530-G-A		not specified	Likely benign (Jan 31, 2024)
19-18929544-G-A		not specified	Uncertain significance (Nov 30, 2021)
19-18929550-G-A		not specified	Uncertain significance (Jun 10, 2022)
19-18929574-C-G		not specified	Uncertain significance (May 05, 2023)
19-18929615-G-A		not specified	Uncertain significance (Aug 08, 2022)
19-18931343-C-A		not specified	Uncertain significance (Jun 05, 2024)
19-18931350-C-T		not specified	Uncertain significance (Aug 09, 2021)
19-18931375-G-A		not specified	Uncertain significance (Dec 05, 2022)
19-18931395-T-C		not specified	Uncertain significance (Dec 12, 2023)
19-18931539-C-T			Benign (Apr 30, 2018)
19-18931578-A-G			Benign (Apr 30, 2018)
19-18931983-C-T		not specified	Uncertain significance (Dec 15, 2023)
19-18931989-C-T		not specified	Uncertain significance (Aug 13, 2021)
19-18932005-G-A		not specified	Uncertain significance (Nov 05, 2021)
19-18932040-G-C		not specified	Uncertain significance (Feb 06, 2024)
19-18932118-A-T		not specified	Uncertain significance (Oct 26, 2021)
19-18933008-C-T		not specified	Uncertain significance (Jun 27, 2022)
19-18933023-C-T		Keratoconus 5	Uncertain significance (May 16, 2024)
19-18933042-G-A		not specified	Uncertain significance (Jul 12, 2022)
19-18933049-G-T			Benign (Apr 30, 2018)
19-18934314-C-T		not specified	Likely benign (Apr 13, 2022)
19-18934344-C-T		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOMER3	protein_coding	protein_coding	ENST00000539827	9	12061

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.954	0.0464	112413	0	1	112414	0.00000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	159	207	0.767	0.0000136	2266
Missense in Polyphen		57	70.033	0.8139		836
Synonymous	1.80	65	86.3	0.753	0.00000564	722
Loss of Function	3.55	2	18.5	0.108	9.50e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000524	0.0000524
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Postsynaptic density scaffolding protein. Binds and cross-links cytoplasmic regions of GRM1, GRM5, ITPR1, DNM3, RYR1, RYR2, SHANK1 and SHANK3. By physically linking GRM1 and GRM5 with ER-associated ITPR1 receptors, it aids the coupling of surface receptors to intracellular calcium release. Isoforms can be differently regulated and may play an important role in maintaining the plasticity at glutamatergic synapses. Negatively regulates T cell activation through negative regulation of IL2 expression by inhibiting calcineurin-NFAT pathway activation through interaction with NFATC2 leading to reduction of interaction between NFATC2 and PPP3CA (PubMed:18218901). {ECO:0000269|PubMed:18218901}.
• Pathway: Glutamatergic synapse - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);TCR;Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.168
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.447
• hipred: Y
• hipred_score: 0.728
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.649

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Homer3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: protein targeting;G protein-coupled glutamate receptor signaling pathway;negative regulation of interleukin-2 production;negative regulation of calcineurin-NFAT signaling cascade;regulation of store-operated calcium entry
• Cellular component: cellular_component;cytoplasm;cytosol;plasma membrane;postsynaptic density;cell junction;dendrite;neuron projection;postsynaptic membrane
• Molecular function: protein binding;G protein-coupled glutamate receptor binding;identical protein binding