LRRC42

leucine rich repeat containing 42

Basic information

Region (hg38): 1:53946077-53968168

Links

ENSG00000116212 ∙ NCBI:115353 ∙ ∙ HGNC:28792 ∙ Uniprot:Q9Y546 ∙ 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 LRRC42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC42 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			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in LRRC42

This is a list of pathogenic ClinVar variants found in the LRRC42 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-53952082-A-T		not specified	Uncertain significance (Oct 04, 2022)
1-53952217-T-C		not specified	Uncertain significance (Apr 05, 2023)
1-53952294-G-A		not specified	Uncertain significance (May 18, 2022)
1-53952309-A-G		not specified	Uncertain significance (Sep 12, 2023)
1-53952319-T-A		not specified	Uncertain significance (May 08, 2024)
1-53952355-T-G		not specified	Uncertain significance (Dec 19, 2022)
1-53952394-G-A		not specified	Uncertain significance (Apr 29, 2024)
1-53958192-C-T		not specified	Uncertain significance (Mar 13, 2023)
1-53958193-G-A		not specified	Uncertain significance (Mar 08, 2024)
1-53960451-A-G		not specified	Uncertain significance (Mar 01, 2024)
1-53962061-T-C		not specified	Uncertain significance (Sep 22, 2023)
1-53962299-A-G		not specified	Likely benign (Oct 17, 2023)
1-53962308-G-A		not specified	Likely benign (Nov 09, 2021)
1-53962338-C-T		not specified	Uncertain significance (Aug 12, 2022)
1-53966374-C-T		not specified	Uncertain significance (Jan 31, 2022)
1-53967722-T-A		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC42	protein_coding	protein_coding	ENST00000371370	7	22092

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-8	0.589	125602	0	146	125748	0.000581

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.219	244	235	1.04	0.0000125	2794
Missense in Polyphen		87	77.357	1.1247		1004
Synonymous	0.703	83	91.6	0.906	0.00000474	841
Loss of Function	1.15	15	20.6	0.727	0.00000126	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00106
Ashkenazi Jewish	0.00512	0.00447
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000495	0.000492
Middle Eastern	0.000544	0.000544
South Asian	0.000230	0.000229
Other	0.000661	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.329
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.36

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.251
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.310

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc42