LRCH4

leucine rich repeats and calponin homology domain containing 4

Basic information

Region (hg38): 7:100574011-100586129

Previous symbols: [ "LRN", "LRRN1" ]

Links

ENSG00000077454 ∙ NCBI:4034 ∙ OMIM:620165 ∙ HGNC:6691 ∙ Uniprot:O75427 ∙ 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 LRCH4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRCH4 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						0
missense			44	3	1	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	44	3	2

Variants in LRCH4

This is a list of pathogenic ClinVar variants found in the LRCH4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100575111-G-C		not specified	Uncertain significance (Jun 06, 2023)
7-100575124-G-A		not specified	Uncertain significance (Sep 14, 2022)
7-100575151-T-C		not specified	Uncertain significance (Oct 06, 2021)
7-100575166-A-C		not specified	Uncertain significance (Apr 26, 2024)
7-100575168-A-C		not specified	Uncertain significance (Aug 12, 2021)
7-100575178-C-T		not specified	Uncertain significance (Apr 09, 2024)
7-100575192-G-C		not specified	Uncertain significance (May 23, 2023)
7-100575204-G-A		not specified	Uncertain significance (Jan 24, 2024)
7-100575207-G-A		not specified	Uncertain significance (Mar 31, 2024)
7-100575222-C-T		not specified	Uncertain significance (Nov 07, 2022)
7-100575252-C-T		not specified	Uncertain significance (Jan 10, 2022)
7-100575261-C-T		not specified	Likely benign (Dec 30, 2023)
7-100575262-G-A		not specified	Uncertain significance (Apr 22, 2022)
7-100575265-C-A		not specified	Uncertain significance (Mar 25, 2024)
7-100575280-G-A		not specified	Uncertain significance (Jun 27, 2022)
7-100575281-A-T		not specified	Uncertain significance (Jun 27, 2022)
7-100575879-G-A		not specified	Uncertain significance (Sep 06, 2022)
7-100575911-G-A		not specified	Uncertain significance (Jun 24, 2022)
7-100575918-G-T		not specified	Uncertain significance (Oct 04, 2022)
7-100576260-T-A		not specified	Uncertain significance (Jan 26, 2023)
7-100576287-C-G		not specified	Uncertain significance (Jul 09, 2021)
7-100576717-C-T		not specified	Uncertain significance (Apr 07, 2022)
7-100576938-G-A		not specified	Uncertain significance (Jul 25, 2023)
7-100577077-G-A			Benign (May 29, 2018)
7-100577108-C-T		not specified	Likely benign (Jun 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRCH4	protein_coding	protein_coding	ENST00000310300	18	13922

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000135	1.00	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.122	436	429	1.02	0.0000285	4236
Missense in Polyphen		158	179.96	0.87796		1800
Synonymous	-0.812	205	191	1.07	0.0000121	1531
Loss of Function	3.08	16	36.0	0.445	0.00000194	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000668	0.000668
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000498	0.0000462
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.000111	0.000109
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.549
• rvis_EVS: -0.88
• rvis_percentile_EVS: 10.5

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.306
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrch4

Gene ontology

• Biological process: nervous system development
• Cellular component: PML body
• Molecular function: protein binding