LRRC72

leucine rich repeat containing 72, the group of Cilia and flagella associated

Basic information

Region (hg38): 7:16526824-16581568

Links

ENSG00000205858 ∙ NCBI:100506049 ∙ ∙ HGNC:42972 ∙ Uniprot:A6NJI9 ∙ 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 LRRC72 gene.

• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC72 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			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	0

Variants in LRRC72

This is a list of pathogenic ClinVar variants found in the LRRC72 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-16527002-T-G		not specified	Uncertain significance (Sep 16, 2022)
7-16527028-C-A		not specified	Uncertain significance (Nov 14, 2023)
7-16527040-C-T		not specified	Uncertain significance (Sep 14, 2022)
7-16532514-A-G		not specified	Uncertain significance (Sep 14, 2022)
7-16532519-T-C		not specified	Likely benign (Nov 08, 2021)
7-16537656-G-A		not specified	Uncertain significance (Sep 23, 2023)
7-16537670-A-G		not specified	Uncertain significance (Mar 20, 2023)
7-16557373-C-T		not specified	Uncertain significance (Nov 30, 2021)
7-16557378-C-A		not specified	Uncertain significance (Dec 20, 2023)
7-16558938-G-C		not specified	Uncertain significance (May 18, 2022)
7-16566345-C-G		not specified	Uncertain significance (Sep 20, 2023)
7-16566352-G-A		not specified	Uncertain significance (Jun 01, 2023)
7-16566364-T-C		not specified	Uncertain significance (Aug 02, 2021)
7-16566397-G-A		not specified	Uncertain significance (Dec 15, 2022)
7-16567471-G-A		not specified	Likely benign (Oct 14, 2021)
7-16581392-C-A		not specified	Uncertain significance (Feb 28, 2023)
7-16581434-A-G		not specified	Uncertain significance (Jul 06, 2021)
7-16581445-G-A		not specified	Likely benign (Feb 28, 2024)
7-16581455-A-T		not specified	Uncertain significance (Nov 02, 2023)
7-16581467-T-G		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC72	protein_coding	protein_coding	ENST00000401542	9	54689

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000278	0.538	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.487	104	119	0.874	0.00000645	1846
Missense in Polyphen		15	24.037	0.62403		443
Synonymous	1.07	35	44.1	0.794	0.00000224	546
Loss of Function	0.792	10	13.1	0.764	8.31e-7	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
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

Haploinsufficiency Scores

• ghis: 0.419

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: Lrrc72