LRRC19

protein-coding

leucine rich repeat containing 19

Gene summary

Predicted to enable signaling receptor activity. Acts upstream of or within positive regulation of non-canonical NF-kappaB signal transduction. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_022901.3

Inheritance

—

ClinVar variants

U:50B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.21

Max pathogenic AF

—

Genomic locus

chr9:26,993,136-27,005,672

External References & Databases

Ensembl (ENSG00000184434)

Transcript & Mutation Effects

hg38 • Region Span ~12.5 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 LRRC19 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 53

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022901.3. 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		2
missense			50 clinvar	8 clinvar		58
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	10	1	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022901.3	RefSeq	NP_075052.1	4	MANE Select
ENST00000380055.6	Ensembl	ENSP00000369395.5	4	MANE Select
ENST00000903358.1	Ensembl	ENSP00000573417.1	4	Standard
ENST00000903358.2	Ensembl	ENSP00000573417.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380055
Coding exons: 4
Length: 12558
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125719
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.436	193	177	1.09	0.00000777	2438
Missense (PolyPhen)		35	36.81	0.95082		531
Synonymous	-1.45	82	66.9	1.23	0.00000310	683
Loss of Function	-0.720	16	13.2	1.21	5.53e-7	195

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.00021	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0641

Intolerance Scores

LoFtool: 0.860
RVIS EVS: 0.73
RVIS percentile EVS: 86.17

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.152

Gene Damage Prediction

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