LRRC19

leucine rich repeat containing 19

Basic information

Region (hg38): 9:26993135-27005672

Links

ENSG00000184434 ∙ NCBI:64922 ∙ OMIM:619068 ∙ HGNC:23379 ∙ Uniprot:Q9H756 ∙ 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 LRRC19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC19 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				1		1
missense			13	3		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	4	0

Variants in LRRC19

This is a list of pathogenic ClinVar variants found in the LRRC19 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-26995552-A-G		not specified	Uncertain significance (Dec 17, 2023)
9-26995598-G-A		not specified	Uncertain significance (Sep 14, 2022)
9-26995659-G-T		not specified	Uncertain significance (Jan 23, 2024)
9-26995676-A-C		not specified	Uncertain significance (May 21, 2024)
9-26995763-T-C		not specified	Uncertain significance (Jun 12, 2023)
9-26995768-A-G		not specified	Uncertain significance (Feb 10, 2022)
9-26995798-G-C		not specified	Uncertain significance (Mar 18, 2024)
9-26995807-A-C		not specified	Uncertain significance (Jun 11, 2021)
9-26995828-C-A		not specified	Uncertain significance (Mar 25, 2024)
9-26996375-A-G			Likely benign (Jul 01, 2023)
9-26996400-G-A		not specified	Uncertain significance (Apr 08, 2024)
9-26996472-T-G		not specified	Uncertain significance (Jan 03, 2024)
9-26997737-C-A		not specified	Uncertain significance (Oct 12, 2021)
9-26997770-A-G		not specified	Likely benign (Jan 06, 2023)
9-26997862-C-T		not specified	Uncertain significance (May 08, 2023)
9-26997899-C-A			Uncertain significance (Jul 01, 2024)
9-26997956-G-C		not specified	Uncertain significance (Dec 13, 2022)
9-26998000-G-A		not specified	Uncertain significance (Nov 18, 2023)
9-26998109-A-G		not specified	Uncertain significance (Mar 16, 2022)
9-26998165-T-G		not specified	Uncertain significance (Jun 02, 2023)
9-26998185-C-A		not specified	Likely benign (Feb 02, 2024)
9-26999682-C-T		not specified	Likely benign (Jul 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC19	protein_coding	protein_coding	ENST00000380055	4	12558

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.19e-12	0.0119	125706	0	13	125719	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.436	193	177	1.09	0.00000777	2438
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000572	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000572	0.0000544
South Asian	0.000205	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0641

Intolerance Scores

• loftool: 0.860
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.17

Haploinsufficiency Scores

• pHI: 0.0566
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.152

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc19

Gene ontology

• Cellular component: integral component of membrane