LRRIQ1

leucine rich repeats and IQ motif containing 1

Basic information

Region (hg38): 12:85036314-85264457

Links

ENSG00000133640 ∙ NCBI:84125 ∙ ∙ HGNC:25708 ∙ Uniprot:Q96JM4 ∙ 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 LRRIQ1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRIQ1 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				1		1
missense			105	7		112
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	105	8	0

Variants in LRRIQ1

This is a list of pathogenic ClinVar variants found in the LRRIQ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-85038190-A-T		not specified	Uncertain significance (Oct 06, 2021)
12-85038211-T-C		not specified	Uncertain significance (Jul 12, 2023)
12-85038217-C-T		not specified	Uncertain significance (Nov 08, 2022)
12-85044795-G-A		not specified	Uncertain significance (Apr 01, 2024)
12-85044802-T-C		not specified	Uncertain significance (Dec 06, 2021)
12-85046032-A-G		not specified	Uncertain significance (Dec 11, 2023)
12-85046065-G-A		not specified	Likely benign (Jul 25, 2023)
12-85046065-G-T		not specified	Uncertain significance (Feb 06, 2024)
12-85046086-G-A		not specified	Uncertain significance (Aug 28, 2023)
12-85046087-T-C		not specified	Uncertain significance (Aug 22, 2022)
12-85047299-G-C		not specified	Uncertain significance (Jul 19, 2022)
12-85047357-C-G		not specified	Uncertain significance (Sep 29, 2023)
12-85047373-A-C		not specified	Uncertain significance (Jan 26, 2023)
12-85047412-G-A		not specified	Uncertain significance (Apr 12, 2024)
12-85047439-T-C		not specified	Uncertain significance (Jan 11, 2023)
12-85052228-A-G		not specified	Uncertain significance (Jan 17, 2024)
12-85052240-A-C		not specified	Uncertain significance (Jan 23, 2023)
12-85055577-G-A		not specified	Uncertain significance (May 27, 2022)
12-85055580-G-A		not specified	Uncertain significance (Jun 03, 2022)
12-85055626-C-A		not specified	Uncertain significance (Jul 12, 2022)
12-85055679-G-A		not specified	Uncertain significance (Dec 06, 2022)
12-85055721-C-G		not specified	Uncertain significance (Jun 14, 2023)
12-85055751-G-A		not specified	Uncertain significance (Nov 02, 2023)
12-85055758-A-T		not specified	Uncertain significance (Sep 01, 2021)
12-85055779-G-A		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRIQ1	protein_coding	protein_coding	ENST00000393217	26	226911

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.52e-37	0.0195	69458	8739	47540	125737	0.257

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.09	882	796	1.11	0.0000377	11366
Missense in Polyphen		187	183.18	1.0209		2723
Synonymous	-0.953	298	278	1.07	0.0000131	2953
Loss of Function	2.04	68	88.7	0.767	0.00000462	1202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.490	0.457
Ashkenazi Jewish	0.338	0.300
East Asian	0.206	0.160
Finnish	0.284	0.260
European (Non-Finnish)	0.327	0.284
Middle Eastern	0.206	0.160
South Asian	0.301	0.248
Other	0.321	0.261

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.997
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.41

Haploinsufficiency Scores

• pHI: 0.0918
• hipred: N
• hipred_score: 0.273

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0426

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrriq1