LRCH3

leucine rich repeats and calponin homology domain containing 3

Basic information

Region (hg38): 3:197791226-197888436

Links

ENSG00000186001 ∙ NCBI:84859 ∙ ∙ HGNC:28637 ∙ Uniprot:Q96II8 ∙ 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 LRCH3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRCH3 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				5	2	7
missense			46	6	1	53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4	1	5
non coding				2		2
Total	0	0	46	13	3

Variants in LRCH3

This is a list of pathogenic ClinVar variants found in the LRCH3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-197791269-C-T		LRCH3-related disorder	Likely benign (Mar 04, 2019)
3-197791284-G-A		LRCH3-related disorder	Likely benign (May 21, 2019)
3-197791302-T-C		LRCH3-related disorder	Likely benign (Sep 10, 2019)
3-197791345-G-A		not specified	Uncertain significance (May 18, 2023)
3-197791357-G-A		not specified	Uncertain significance (Dec 17, 2023)
3-197791364-A-C		not specified	Uncertain significance (Nov 22, 2022)
3-197791385-C-A		not specified	Uncertain significance (Jul 11, 2023)
3-197791387-G-A		not specified	Uncertain significance (May 15, 2024)
3-197791405-G-T		not specified	Uncertain significance (Feb 27, 2023)
3-197791432-G-T		not specified	Uncertain significance (Feb 21, 2024)
3-197791433-C-G		not specified	Uncertain significance (Jun 17, 2024)
3-197791477-C-T		not specified	Uncertain significance (Jan 03, 2024)
3-197791495-C-T		not specified	Uncertain significance (Jan 23, 2023)
3-197791502-G-A		not specified	Uncertain significance (Feb 28, 2024)
3-197791534-C-T		not specified	Uncertain significance (Feb 12, 2024)
3-197814905-T-C		LRCH3-related disorder	Likely benign (Jul 17, 2019)
3-197814925-C-T		not specified	Uncertain significance (Feb 03, 2022)
3-197817211-G-A		LRCH3-related disorder	Likely benign (Feb 10, 2022)
3-197817244-A-G		not specified	Uncertain significance (Dec 14, 2022)
3-197817274-T-C		not specified	Uncertain significance (Oct 12, 2022)
3-197817276-G-C		not specified	Uncertain significance (Mar 31, 2023)
3-197817289-A-G		not specified	Uncertain significance (Dec 07, 2023)
3-197820410-A-C		not specified	Uncertain significance (Oct 26, 2022)
3-197826887-A-G		not specified	Uncertain significance (Nov 17, 2023)
3-197826899-T-A		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRCH3	protein_coding	protein_coding	ENST00000334859	19	97211

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.63e-12	0.991	125640	0	108	125748	0.000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.278	371	386	0.960	0.0000204	4552
Missense in Polyphen		115	128.36	0.89591		1478
Synonymous	0.301	145	150	0.969	0.00000808	1441
Loss of Function	2.54	25	43.0	0.582	0.00000239	485

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00107
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.0000544	0.0000544
Finnish	0.000240	0.000231
European (Non-Finnish)	0.000416	0.000413
Middle Eastern	0.0000544	0.0000544
South Asian	0.000523	0.000523
Other	0.000977	0.000978

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0981

Intolerance Scores

• loftool: 0.842
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.82

Haploinsufficiency Scores

• pHI: 0.254
• hipred: N
• hipred_score: 0.379
• ghis: 0.631

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.694

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrch3

Gene ontology

• Cellular component: extracellular region;cytosol
• Molecular function: protein binding