LRCH2

leucine rich repeats and calponin homology domain containing 2

Basic information

Region (hg38): X:115110616-115234096

Links

ENSG00000130224 ∙ NCBI:57631 ∙ ∙ HGNC:29292 ∙ Uniprot:Q5VUJ6 ∙ 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 LRCH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRCH2 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				3		3
missense			19	1		20
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			122	21		143
Total	0	0	142	25	0

Variants in LRCH2

This is a list of pathogenic ClinVar variants found in the LRCH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-115113264-C-A			Likely benign (Oct 01, 2022)
X-115113290-C-T		not specified	Uncertain significance (Apr 05, 2023)
X-115122768-G-A		not specified	Uncertain significance (Aug 02, 2021)
X-115122786-T-C		not specified	Uncertain significance (Jun 02, 2023)
X-115122807-T-C			Likely benign (Apr 01, 2023)
X-115123094-G-A			Uncertain significance (Sep 14, 2023)
X-115126865-G-A		not specified	Uncertain significance (May 17, 2023)
X-115126866-T-C		not specified	Uncertain significance (Mar 25, 2024)
X-115130162-T-A		not specified	Uncertain significance (Oct 28, 2023)
X-115130190-T-C		not specified	Uncertain significance (Aug 17, 2021)
X-115149886-T-C		not specified	Uncertain significance (Apr 13, 2022)
X-115149894-G-A		not specified	Uncertain significance (Jun 03, 2022)
X-115156614-T-A		not specified	Uncertain significance (Dec 07, 2021)
X-115165438-G-A		not specified	Uncertain significance (Jun 11, 2021)
X-115165647-C-A		not specified	Uncertain significance (Dec 13, 2021)
X-115165892-T-A		not specified	Uncertain significance (Feb 28, 2023)
X-115165928-G-C		not specified	Uncertain significance (May 29, 2024)
X-115165930-C-T		not specified	Uncertain significance (Feb 16, 2023)
X-115166309-G-C			Likely benign (Aug 01, 2022)
X-115170306-T-C		not specified	Uncertain significance (Jul 06, 2021)
X-115170326-C-T		not specified	Uncertain significance (Oct 25, 2023)
X-115179519-T-C		Demyelinating peripheral neuropathy;Cerebellar ataxia	Pathogenic (-)
X-115188356-G-A		not specified	Uncertain significance (Jul 07, 2022)
X-115189446-T-C		not specified	Uncertain significance (Feb 22, 2023)
X-115189478-G-A		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRCH2	protein_coding	protein_coding	ENST00000317135	21	123451

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00287	108989	0	1	108990	0.00000459

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	138	219	0.631	0.0000156	4934
Missense in Polyphen		50	98.25	0.50891		2179
Synonymous	1.24	64	77.9	0.822	0.00000524	1427
Loss of Function	4.36	2	26.0	0.0769	0.00000205	578

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000153	0.000119
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0936

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.161
• hipred: Y
• hipred_score: 0.657
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrch2
• Phenotype: normal phenotype