GeneBe

LIN7C

lin-7 homolog C, crumbs cell polarity complex component, the group of PDZ domain containing|Crumbs complex

Basic information

Region (hg38): 11:27494418-27506769

Links

ENSG00000148943 ∙ NCBI:55327 ∙ OMIM:612332 ∙ HGNC:17789 ∙ Uniprot:Q9NUP9 ∙ 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 LIN7C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIN7C 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
0
missense
6
clinvar
 6
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 6 0 0

Variants in LIN7C

This is a list of pathogenic ClinVar variants found in the LIN7C region.

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

Position Type Phenotype Significance ClinVar
11-27498695-G-A not specified Uncertain significance (May 04, 2023)2525508
11-27498708-C-T not specified Uncertain significance (Nov 18, 2023)3118948
11-27499442-T-C not specified Uncertain significance (Dec 06, 2023)3118946
11-27501879-T-C not specified Uncertain significance (Nov 07, 2023)3118950
11-27506718-C-G not specified Uncertain significance (Dec 11, 2023)3118947
11-27506731-C-T not specified Uncertain significance (Nov 03, 2023)3118945

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LIN7Cprotein_codingprotein_codingENST00000278193 512198
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.05130.9301257261201257470.0000835
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.09771090.7070.000005551266
Missense in Polyphen3152.2510.59329606
Synonymous-0.4964339.11.100.00000201394
Loss of Function2.04411.40.3506.99e-7126

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006150.0000615
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.0002770.000231
European (Non-Finnish)0.00005290.0000527
Middle Eastern0.00005440.0000544
South Asian0.0001960.000196
Other0.0003260.000326

dbNSFP

Source: dbNSFP

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.;
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
0.156

Intolerance Scores

loftool
0.553
rvis_EVS
-0.25
rvis_percentile_EVS
35.42

Haploinsufficiency Scores

pHI
0.644
hipred
Y
hipred_score
0.754
ghis
0.698

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
E
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.925

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Lin7c
Phenotype
growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; renal/urinary system phenotype; respiratory system phenotype; normal 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); 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);

Zebrafish Information Network

Gene name
lin7c
Affected structure
neuroepithelial cell
Phenotype tag
abnormal
Phenotype quality
apical-basal polarity

Gene ontology

Biological process
morphogenesis of an epithelial sheet;exocytosis;neurotransmitter secretion;protein transport;maintenance of epithelial cell apical/basal polarity;protein localization to basolateral plasma membrane
Cellular component
cytoplasm;plasma membrane;cell-cell junction;bicellular tight junction;postsynaptic density;basolateral plasma membrane;neuron projection;synapse;postsynaptic membrane;MPP7-DLG1-LIN7 complex;presynapse;glutamatergic synapse
Molecular function
cytoskeletal protein binding;protein domain specific binding;PDZ domain binding;L27 domain binding