LIN7A
lin-7 homolog A, crumbs cell polarity complex component, the group of PDZ domain containing|MicroRNA protein coding host genes|Crumbs complex
Basic information
Region (hg38): 12:80792520-80937934
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 LIN7A 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 | |||||
| missense | 9 | |||||
| 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 | 9 | 0 | 1 |
Variants in LIN7A
This is a list of pathogenic ClinVar variants found in the LIN7A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-80811516-C-A | not specified | Uncertain significance (Jul 12, 2023) | ||
| 12-80811544-C-T | not specified | Uncertain significance (Sep 24, 2024) | ||
| 12-80811600-G-T | Benign (Dec 31, 2019) | |||
| 12-80845785-G-A | not specified | Uncertain significance (Aug 12, 2022) | ||
| 12-80845789-C-T | not specified | Uncertain significance (Oct 26, 2022) | ||
| 12-80845798-G-A | not specified | Uncertain significance (Feb 09, 2023) | ||
| 12-80845813-T-C | not specified | Uncertain significance (Nov 30, 2021) | ||
| 12-80845874-C-A | not specified | Uncertain significance (Jun 28, 2024) | ||
| 12-80845942-GA-G | not specified | Benign (Jul 15, 2015) | ||
| 12-80848277-C-T | not specified | Uncertain significance (Jan 17, 2024) | ||
| 12-80937665-C-T | not specified | Uncertain significance (Aug 02, 2021) | ||
| 12-80937695-G-A | not specified | Uncertain significance (Oct 30, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LIN7A | protein_coding | protein_coding | ENST00000552864 | 5 | 145406 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.13e-7 | 0.348 | 125735 | 0 | 13 | 125748 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.20 | 91 | 129 | 0.704 | 0.00000710 | 1491 |
| Missense in Polyphen | 19 | 28.494 | 0.6668 | 299 | ||
| Synonymous | 0.929 | 40 | 48.2 | 0.830 | 0.00000256 | 475 |
| Loss of Function | 0.610 | 12 | 14.5 | 0.827 | 9.12e-7 | 142 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000970 | 0.0000970 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.0000530 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000981 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in establishing and maintaining the asymmetric distribution of channels and receptors at the plasma membrane of polarized cells. Forms membrane-associated multiprotein complexes that may regulate delivery and recycling of proteins to the correct membrane domains. The tripartite complex composed of LIN7 (LIN7A, LIN7B or LIN7C), CASK and APBA1 may have the potential to couple synaptic vesicle exocytosis to cell adhesion in brain. Ensures the proper localization of GRIN2B (subunit 2B of the NMDA receptor) to neuronal postsynaptic density and may function in localizing synaptic vesicles at synapses where it is recruited by beta-catenin and cadherin. Required to localize Kir2 channels, GABA transporter (SLC6A12) and EGFR/ERBB1, ERBB2, ERBB3 and ERBB4 to the basolateral membrane of epithelial cells. {ECO:0000269|PubMed:12967566}.;
- Pathway
- Neuronal System;Dopamine Neurotransmitter Release Cycle;Neurotransmitter release cycle;Neurexins and neuroligins;Transmission across Chemical Synapses;Protein-protein interactions at synapses
(Consensus)
Recessive Scores
- pRec
- 0.221
Intolerance Scores
- loftool
- 0.674
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.441
- hipred
- Y
- hipred_score
- 0.653
- ghis
- 0.588
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lin7a
- 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); respiratory 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); normal phenotype;
Gene ontology
- Biological process
- exocytosis;neurotransmitter secretion;protein transport;maintenance of epithelial cell apical/basal polarity;synaptic vesicle transport;inner ear development;protein-containing complex assembly;protein localization to basolateral plasma membrane
- Cellular component
- plasma membrane;cell-cell junction;bicellular tight junction;postsynaptic density;basolateral plasma membrane;neuron projection;synapse;postsynaptic membrane;extracellular exosome;MPP7-DLG1-LIN7 complex;presynapse
- Molecular function
- protein binding;L27 domain binding