LRRC73

leucine rich repeat containing 73

Basic information

Region (hg38): 6:43506967-43510346

Previous symbols: [ "C6orf154" ]

Links

ENSG00000204052 ∙ NCBI:221424 ∙ ∙ HGNC:21375 ∙ Uniprot:Q5JTD7 ∙ 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 LRRC73 gene.

• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC73 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			12
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	0	0

Variants in LRRC73

This is a list of pathogenic ClinVar variants found in the LRRC73 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-43507263-C-T		not specified	Uncertain significance (Jan 12, 2024)
6-43507272-A-G		not specified	Uncertain significance (Feb 23, 2023)
6-43507468-T-A		not specified	Uncertain significance (Nov 30, 2021)
6-43507587-A-G		not specified	Uncertain significance (May 26, 2023)
6-43507605-G-A		not specified	Uncertain significance (Feb 28, 2023)
6-43507639-G-A		not specified	Uncertain significance (Dec 19, 2023)
6-43508363-C-A		not specified	Uncertain significance (May 30, 2023)
6-43508810-T-G		not specified	Uncertain significance (Nov 17, 2022)
6-43508816-C-A		not specified	Uncertain significance (Jan 10, 2023)
6-43508834-A-C		not specified	Uncertain significance (Feb 16, 2023)
6-43508906-G-A		not specified	Uncertain significance (May 30, 2023)
6-43509620-T-C		not specified	Uncertain significance (Apr 28, 2022)
6-43509628-G-T		not specified	Uncertain significance (Sep 12, 2023)
6-43509698-C-G		not specified	Uncertain significance (Oct 10, 2023)
6-43509740-C-T		not specified	Uncertain significance (Mar 14, 2023)
6-43509763-A-G		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC73	protein_coding	protein_coding	ENST00000372441	6	3718

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0487	0.931	125699	0	11	125710	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.62	124	186	0.666	0.00000962	2009
Missense in Polyphen		29	40.496	0.71612		481
Synonymous	-1.44	97	80.6	1.20	0.00000420	691
Loss of Function	2.01	4	11.3	0.354	4.81e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000627	0.0000616
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.585
• hipred: Y
• hipred_score: 0.650
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc73