LRRC7

leucine rich repeat containing 7, the group of PDZ domain containing

Basic information

Region (hg38): 1:69567922-70151945

Links

ENSG00000033122 ∙ NCBI:57554 ∙ OMIM:614453 ∙ HGNC:18531 ∙ Uniprot:Q96NW7 ∙ 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 LRRC7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC7 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			57	1		58
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	60	3	0

Variants in LRRC7

This is a list of pathogenic ClinVar variants found in the LRRC7 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-69678414-G-A			Likely benign (Dec 01, 2022)
1-69760265-G-C			Uncertain significance (Feb 08, 2023)
1-69792096-T-C			Likely benign (Dec 01, 2022)
1-69825799-T-C			Uncertain significance (May 23, 2023)
1-69834794-T-C		not specified	Uncertain significance (Apr 13, 2022)
1-69931516-C-G		not specified	Uncertain significance (Apr 13, 2022)
1-69931562-G-A		not specified	Likely benign (Feb 08, 2023)
1-69986241-G-T			Uncertain significance (Feb 16, 2023)
1-69986354-C-T		not specified	Uncertain significance (Dec 27, 2022)
1-70011809-A-G			Uncertain significance (Nov 10, 2023)
1-70011852-T-G		not specified	Uncertain significance (Sep 12, 2023)
1-70012972-A-G			Uncertain significance (May 03, 2023)
1-70013013-T-TC			Uncertain significance (Mar 12, 2024)
1-70013044-T-C			Uncertain significance (Apr 01, 2023)
1-70016517-T-C			Uncertain significance (Apr 04, 2024)
1-70021067-A-G		not specified	Uncertain significance (Oct 30, 2023)
1-70023135-T-G		not specified	Uncertain significance (Mar 31, 2022)
1-70023145-C-T		not specified	Uncertain significance (Apr 14, 2022)
1-70023157-GC-G			Uncertain significance (Apr 21, 2024)
1-70023183-G-T		not specified	Uncertain significance (Dec 27, 2022)
1-70023198-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-70023285-A-G		not specified	Uncertain significance (Mar 19, 2024)
1-70023336-G-C		not specified	Uncertain significance (Aug 08, 2022)
1-70023355-C-T		not specified	Uncertain significance (Jun 02, 2023)
1-70028214-A-G		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC7	protein_coding	protein_coding	ENST00000035383	25	583548

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.16e-8	125644	0	57	125701	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.60	533	824	0.647	0.0000434	10118
Missense in Polyphen		209	400.01	0.52249		5182
Synonymous	-0.140	310	307	1.01	0.0000167	2923
Loss of Function	7.39	6	75.2	0.0798	0.00000384	910

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000545
Finnish	0.000327	0.000323
European (Non-Finnish)	0.000389	0.000387
Middle Eastern	0.0000546	0.0000545
South Asian	0.0000328	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for normal synaptic spine architecture and function. Necessary for DISC1 and GRM5 localization to postsynaptic density complexes and for both N-methyl D-aspartate receptor-dependent and metabotropic glutamate receptor-dependent long term depression. {ECO:0000269|PubMed:11729199}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.209
• rvis_EVS: -1.37
• rvis_percentile_EVS: 4.48

Haploinsufficiency Scores

• pHI: 0.426
• hipred: Y
• hipred_score: 0.765
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.872

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc7
• Phenotype: growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: MAPK cascade;positive regulation of neuron projection development;receptor clustering;neutrophil degranulation;establishment or maintenance of epithelial cell apical/basal polarity;receptor localization to synapse;cell-cell adhesion;neurotransmitter receptor transport, endosome to postsynaptic membrane;neurotransmitter receptor transport postsynaptic membrane to endosome
• Cellular component: extracellular region;cytosol;cell-cell junction;cell-cell adherens junction;ionotropic glutamate receptor complex;postsynaptic density;basolateral plasma membrane;cell junction;specific granule lumen;neuron projection;axon initial segment;synapse;postsynaptic membrane
• Molecular function: Ras guanyl-nucleotide exchange factor activity;protein binding;ionotropic glutamate receptor binding