LRRIQ3

leucine rich repeats and IQ motif containing 3

Basic information

Region (hg38): 1:74026015-74198187

Previous symbols: [ "LRRC44" ]

Links

ENSG00000162620 ∙ NCBI:127255 ∙ OMIM:617957 ∙ HGNC:28318 ∙ Uniprot:A6PVS8 ∙ 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 LRRIQ3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRIQ3 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			33	5	6	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1	1		2
splice region				1		1
non coding						0
Total	0	0	34	9	6

Variants in LRRIQ3

This is a list of pathogenic ClinVar variants found in the LRRIQ3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-74026887-G-C		not specified	Uncertain significance (Feb 05, 2024)
1-74026932-A-T		not specified	Uncertain significance (Aug 26, 2022)
1-74026949-C-T		not specified	Uncertain significance (Oct 18, 2021)
1-74026956-A-G		not specified	Likely benign (Sep 17, 2021)
1-74041209-C-T			Likely benign (Dec 31, 2019)
1-74041242-C-A		not specified	Uncertain significance (Nov 12, 2021)
1-74041292-C-G		not specified	Uncertain significance (Sep 27, 2022)
1-74041357-C-T		not specified	Uncertain significance (Dec 05, 2022)
1-74041358-G-A		LRRIQ3-related disorder	Benign (Feb 28, 2019)
1-74041361-C-T		not specified	Uncertain significance (Nov 13, 2023)
1-74041439-T-C		not specified	Uncertain significance (Jan 20, 2023)
1-74041454-A-T		not specified	Uncertain significance (Mar 24, 2023)
1-74041475-C-T		not specified	Uncertain significance (May 12, 2024)
1-74041482-T-G			Benign (Dec 31, 2019)
1-74041496-T-G		not specified	Uncertain significance (May 24, 2024)
1-74041501-T-A		not specified	Uncertain significance (Jul 12, 2022)
1-74041624-T-C		not specified	Uncertain significance (May 13, 2024)
1-74041717-T-G		not specified	Uncertain significance (Nov 18, 2022)
1-74041727-G-A		not specified	Conflicting classifications of pathogenicity (Apr 01, 2024)
1-74041739-T-C		LRRIQ3-related disorder	Benign (Dec 31, 2019)
1-74041767-A-C		LRRIQ3-related disorder	Likely benign (Mar 04, 2019)
1-74041782-C-A		not specified	Uncertain significance (Dec 16, 2023)
1-74041809-T-A		not specified	Uncertain significance (Dec 14, 2023)
1-74041832-T-A		not specified	Uncertain significance (Mar 04, 2024)
1-74041858-A-G		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRIQ3	protein_coding	protein_coding	ENST00000354431	7	172173

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.37e-13	0.0920	125520	2	182	125704	0.000732

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.824	327	288	1.14	0.0000133	4116
Missense in Polyphen		58	48.619	1.1929		730
Synonymous	-0.555	103	96.1	1.07	0.00000423	1082
Loss of Function	0.685	22	25.7	0.854	0.00000149	354

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00795	0.00710
Ashkenazi Jewish	0.00	0.00
East Asian	0.000343	0.000326
Finnish	0.000240	0.000231
European (Non-Finnish)	0.000308	0.000290
Middle Eastern	0.000343	0.000326
South Asian	0.000468	0.000392
Other	0.000595	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.966
• rvis_EVS: 1.38
• rvis_percentile_EVS: 94.6

Haploinsufficiency Scores

• pHI: 0.0692
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0000400

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrriq3

Gene ontology

• Molecular function: protein binding