LIN7B

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

Basic information

Region (hg38): 19:49114324-49118460

Links

ENSG00000104863 ∙ NCBI:64130 ∙ OMIM:612331 ∙ HGNC:17788 ∙ Uniprot:Q9HAP6 ∙ 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 LIN7B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIN7B 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		2	3
non coding						0
Total	0	0	13	2	0

Variants in LIN7B

This is a list of pathogenic ClinVar variants found in the LIN7B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49114424-C-T		not specified	Uncertain significance (Apr 08, 2024)
19-49114439-G-C		not specified	Uncertain significance (Jan 23, 2024)
19-49114449-T-C		LIN7B-related disorder	Benign (Feb 05, 2020)
19-49114858-G-A		not specified	Uncertain significance (Jun 16, 2022)
19-49114875-G-C		not specified	Uncertain significance (Sep 12, 2023)
19-49114903-C-T		not specified	Uncertain significance (May 31, 2023)
19-49114920-G-A		not specified	Uncertain significance (Aug 17, 2021)
19-49114961-C-G		not specified	Uncertain significance (Oct 12, 2021)
19-49114975-G-C			Uncertain significance (Sep 03, 2021)
19-49115283-G-T		LIN7B-related disorder	Likely benign (Oct 28, 2019)
19-49115302-G-A		not specified	Uncertain significance (Jun 05, 2024)
19-49115304-C-A		LIN7B-related disorder	Likely benign (Mar 05, 2019)
19-49115318-A-G		not specified	Uncertain significance (Mar 14, 2023)
19-49115324-C-T		not specified	Uncertain significance (May 14, 2024)
19-49116304-T-G		not specified	Uncertain significance (Jan 03, 2024)
19-49116318-A-G		not specified	Uncertain significance (Mar 07, 2024)
19-49116330-C-T		not specified	Uncertain significance (Dec 30, 2023)
19-49116467-G-C		not specified	Uncertain significance (May 23, 2024)
19-49117865-G-T		not specified	Uncertain significance (Dec 02, 2022)
19-49117889-A-G		not specified	Uncertain significance (Apr 01, 2024)
19-49117927-G-C		not specified	Uncertain significance (Jan 22, 2024)
19-49117930-C-A		not specified	Uncertain significance (May 30, 2024)
19-49117991-G-A		not specified	Uncertain significance (Jul 12, 2022)
19-49118344-C-G			Benign (Jun 21, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIN7B	protein_coding	protein_coding	ENST00000221459	6	4137

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.854	0.146	125729	0	10	125739	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	90	124	0.728	0.00000835	1287
Missense in Polyphen		25	47.986	0.52099		464
Synonymous	-0.0364	51	50.7	1.01	0.00000339	439
Loss of Function	2.74	1	10.7	0.0936	7.15e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000710	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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. May increase the amplitude of ASIC3 acid-evoked currents by stabilizing the channel at the cell surface (By similarity). {ECO:0000250, ECO:0000269|PubMed:11742811}.
• Pathway: Signal Transduction;RHO GTPases Activate Rhotekin and Rhophilins;Neuronal System;RHO GTPase Effectors;Signaling by Rho GTPases;Dopamine Neurotransmitter Release Cycle;Neurotransmitter release cycle;Neurexins and neuroligins;Transmission across Chemical Synapses;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.396
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.263
• hipred: Y
• hipred_score: 0.785
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lin7b
• 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); 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; respiratory system phenotype

Gene ontology

• Biological process: exocytosis;neurotransmitter secretion;protein transport;maintenance of epithelial cell apical/basal polarity;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;MPP7-DLG1-LIN7 complex;presynapse
• Molecular function: protein domain specific binding;PDZ domain binding;L27 domain binding