LRCH4

protein-coding

leucine rich repeats and calponin homology domain containing 4

Gene summary

This gene encodes a protein that contains leucine-rich repeats (LRR) at its amino terminus and that is known to be involved in ligand binding. The carboxyl terminus may act as a membrane anchor. Identified structural elements suggest that the encoded protein resembles a receptor. [provided by RefSeq, Jul 2008]

Previous symbols:

LRN
LRRN1

MANE transcript

NM_002319.5

Inheritance

—

ClinVar variants

U:151B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr7:100,574,011-100,586,129

External References & Databases

Ensembl (ENSG00000077454)

Transcript & Mutation Effects

hg38 • Region Span ~12.1 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 LRCH4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 138

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002319.5. 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			2 clinvar	1 clinvar		3
missense			138 clinvar	7 clinvar	1 clinvar	146
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	151	8	1	160

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 77 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002319.5	RefSeq	NP_002310.2	18	MANE Select
ENST00000310300.11	Ensembl	ENSP00000309689.6	18	MANE Select
NM_001289934.2	RefSeq	NP_001276863.1	18	Standard
ENST00000485554.6	Ensembl	ENSP00000419674.2	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

nervous system development

Molecular Function

protein binding

Cellular Component

PML body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000310300
Coding exons: 18
Length: 13922
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 36
Defined: 125748
p: 0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.122	436	429	1.02	0.0000285	4236
Missense (PolyPhen)		158	179.96	0.87796		1800
Synonymous	-0.812	205	191	1.07	0.0000121	1531
Loss of Function	3.08	16	36.0	0.445	0.00000194	376

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000050	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00023	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.135

Intolerance Scores

LoFtool: 0.549
RVIS EVS: -0.88
RVIS percentile EVS: 10.5

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.991

Gene Damage Prediction

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