LRRC4C

protein-coding

leucine rich repeat containing 4C, the group of Ig-like cell adhesion molecule family|I-set domain containing

Gene summary

NGL1 is a specific binding partner for netrin G1 (NTNG1; MIM 608818), which is a member of the netrin family of axon guidance molecules (Lin et al., 2003 [PubMed 14595443]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_001258419.2

Inheritance

—

ClinVar variants

U:57B:2

Top phenotype

LRRC4C-related disorder

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr11:40,114,203-41,459,773

External References & Databases

Ensembl (ENSG00000148948)

Transcript & Mutation Effects

hg38 • Region Span ~1,345.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LRRC4C variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 53

LRRC4C-related disorderTotal: 4

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001258419.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			56 clinvar	1 clinvar		57
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	2	0	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001258419.2	RefSeq	NP_001245348.1	1	MANE Select
ENST00000528697.6	Ensembl	ENSP00000437132.1	1	MANE Select
NM_020929.3	RefSeq	NP_065980.1	1	Standard
ENST00000278198.2	Ensembl	ENSP00000278198.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cell adhesion molecules (CAMs) - Homo sapiens (human)
Axon guidance - Homo sapiens (human)

Biological Process

regulation of axonogenesis
modulation of chemical synaptic transmission
synaptic membrane adhesion

Molecular Function

protein binding
cell adhesion molecule binding
cell-cell adhesion mediator activity

Cellular Component

extracellular space
membrane
integral component of membrane
cell junction
Schaffer collateral - CA1 synapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000278198
Coding exons: 1
Length: 1345571
Individuals with no LoFs: 125725
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125730
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.52	224	358	0.625	0.0000197	4220
Missense (PolyPhen)		50	119.97	0.41678		1450
Synonymous	-0.302	143	138	1.03	0.00000752	1320
Loss of Function	3.41	1	15.5	0.0646	9.17e-7	184

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May promote neurite outgrowth of developing thalamic neurons. {ECO:0000269|PubMed:14595443}.;

Recessive Scores

pRec: 0.142

Intolerance Scores

LoFtool: 0.0242
RVIS EVS: -0.8
RVIS percentile EVS: 12.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.858

Gene Damage Prediction

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