HOMER1
homer scaffold protein 1, the group of Homer scaffold proteins
Basic information
Region (hg38): 5:79372636-79514134
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOMER1 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 | 3 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 2 | |||||
| Total | 0 | 0 | 7 | 1 | 4 |
Variants in HOMER1
This is a list of pathogenic ClinVar variants found in the HOMER1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-79376070-C-A | not specified | Uncertain significance (Sep 17, 2021) | ||
| 5-79376107-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
| 5-79396864-C-T | not specified | Uncertain significance (Mar 06, 2023) | ||
| 5-79397545-T-G | Likely benign (Jun 18, 2018) | |||
| 5-79401890-T-C | Benign (Jun 08, 2018) | |||
| 5-79401974-C-T | Benign (Jul 30, 2018) | |||
| 5-79439026-A-G | Benign (Mar 29, 2018) | |||
| 5-79439109-T-G | not specified | Uncertain significance (Feb 23, 2023) | ||
| 5-79447064-T-C | not specified | Uncertain significance (Jun 21, 2023) | ||
| 5-79447069-G-A | not specified | Uncertain significance (Aug 15, 2023) | ||
| 5-79450980-T-C | Benign (Aug 24, 2018) | |||
| 5-79451031-C-T | not specified | Uncertain significance (Jun 17, 2024) | ||
| 5-79451082-T-C | not specified | Uncertain significance (Nov 08, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HOMER1 | protein_coding | protein_coding | ENST00000334082 | 9 | 141582 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000803 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.43 | 93 | 186 | 0.500 | 0.00000963 | 2329 |
| Missense in Polyphen | 19 | 70.259 | 0.27043 | 911 | ||
| Synonymous | 0.834 | 59 | 67.7 | 0.871 | 0.00000342 | 658 |
| Loss of Function | 4.21 | 0 | 20.6 | 0.00 | 9.41e-7 | 248 |
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 | 0.00 | 0.00 |
| 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:
- 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. May also couple GRM1 to PI3 kinase through its interaction with AGAP2. Isoform 1 regulates the trafficking and surface expression of GRM5. Isoform 3 acts as a natural dominant negative, in dynamic competition with constitutively expressed isoform 1 to regulate synaptic metabotropic glutamate function. Isoform 3, may be involved in the structural changes that occur at synapses during long-lasting neuronal plasticity and development. Forms a high-order complex with SHANK1, which in turn is necessary for the structural and functional integrity of dendritic spines (By similarity). {ECO:0000250|UniProtKB:Q9Z214}.;
- Pathway
- Glutamatergic synapse - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);BDNF-TrkB Signaling;Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses
(Consensus)
Recessive Scores
- pRec
- 0.168
Intolerance Scores
- loftool
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.42
Haploinsufficiency Scores
- pHI
- 0.781
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.648
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.839
Mouse Genome Informatics
- Gene name
- Homer1
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism 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); endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- homer1b
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- shortened
Gene ontology
- Biological process
- skeletal muscle contraction;phospholipase C-activating G protein-coupled glutamate receptor signaling pathway;G protein-coupled glutamate receptor signaling pathway;chemical synaptic transmission;positive regulation of signal transduction;behavioral response to cocaine;skeletal muscle fiber development;chemical homeostasis within a tissue;protein tetramerization;response to calcium ion;positive regulation of calcium ion transport;regulation of synaptic transmission, glutamatergic;regulation of calcium ion import;regulation of postsynaptic neurotransmitter receptor activity;regulation of dendritic spine maintenance;regulation of store-operated calcium entry;regulation of cation channel activity
- Cellular component
- cytoplasm;cytosol;plasma membrane;postsynaptic density;Z disc;cell junction;axon;dendrite;neuron projection;costamere;dendritic spine;neuron spine;apical part of cell;postsynaptic membrane;glutamatergic synapse;postsynaptic cytosol
- Molecular function
- protein binding;G protein-coupled glutamate receptor binding;signaling adaptor activity;ion channel binding