LRCH1

leucine rich repeats and calponin homology domain containing 1

Basic information

Region (hg38): 13:46553168-46753040

Previous symbols: [ "CHDC1" ]

Links

ENSG00000136141 ∙ NCBI:23143 ∙ OMIM:610368 ∙ HGNC:20309 ∙ Uniprot:Q9Y2L9 ∙ 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 LRCH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRCH1 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			48		1	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	0	2

Variants in LRCH1

This is a list of pathogenic ClinVar variants found in the LRCH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-46553434-C-T		not specified	Uncertain significance (May 27, 2022)
13-46553452-C-T		not specified	Uncertain significance (Jun 02, 2023)
13-46553471-T-G		not specified	Uncertain significance (Dec 14, 2022)
13-46553533-G-A		not specified	Uncertain significance (Jun 27, 2023)
13-46553538-G-C		not specified	Uncertain significance (Dec 12, 2023)
13-46553556-G-T		not specified	Uncertain significance (Mar 30, 2022)
13-46553557-G-T		not specified	Uncertain significance (May 12, 2024)
13-46553668-C-T		not specified	Uncertain significance (Jan 26, 2022)
13-46669091-G-A		not specified	Uncertain significance (Oct 27, 2021)
13-46681744-G-A		not specified	Uncertain significance (Jul 27, 2021)
13-46681766-C-T		not specified	Uncertain significance (May 18, 2023)
13-46681793-A-T		not specified	Uncertain significance (Feb 07, 2023)
13-46681802-G-A		not specified	Uncertain significance (Dec 09, 2023)
13-46681831-A-C		not specified	Uncertain significance (Jun 06, 2022)
13-46685958-G-A		not specified	Uncertain significance (May 30, 2024)
13-46685996-A-G			Benign (May 09, 2018)
13-46686019-C-T		not specified	Uncertain significance (Dec 08, 2023)
13-46687881-T-G		not specified	Uncertain significance (Feb 07, 2023)
13-46687891-A-C		not specified	Uncertain significance (Dec 06, 2021)
13-46687892-G-A		not specified	Uncertain significance (Dec 04, 2023)
13-46687894-A-G		not specified	Uncertain significance (Jul 30, 2023)
13-46687908-G-C		not specified	Uncertain significance (Mar 01, 2023)
13-46687930-T-C		not specified	Uncertain significance (Jun 05, 2024)
13-46692545-G-A		not specified	Uncertain significance (Jun 16, 2024)
13-46692576-C-T		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRCH1	protein_coding	protein_coding	ENST00000389797	20	199873

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00448	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	334	413	0.808	0.0000215	4982
Missense in Polyphen		115	174.03	0.6608		2159
Synonymous	0.739	148	160	0.926	0.00000901	1462
Loss of Function	5.18	6	42.5	0.141	0.00000227	491

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00185	0.00185
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.00185	0.00185
South Asian	0.00	0.00
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a negative regulator of GTPase CDC42 by sequestering CDC42-guanine exchange factor DOCK8. Probably by preventing CDC42 activation, negatively regulates CD4(+) T-cell migration. {ECO:0000269|PubMed:28028151}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.161
• rvis_EVS: 0
• rvis_percentile_EVS: 54.07

Haploinsufficiency Scores

• pHI: 0.166
• hipred: Y
• hipred_score: 0.543
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.672

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrch1
• Phenotype: hematopoietic system phenotype; immune system phenotype; cellular phenotype

Gene ontology

• Biological process: negative regulation of GTPase activity;cellular response to chemokine;negative regulation of T cell migration
• Cellular component: cytoplasm
• Molecular function: protein binding