LRRIQ4

leucine rich repeats and IQ motif containing 4

Basic information

Region (hg38): 3:169812870-169837773

Links

ENSG00000188306 ∙ NCBI:344657 ∙ ∙ HGNC:34298 ∙ Uniprot:A6NIV6 ∙ 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 LRRIQ4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRIQ4 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			41	2		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	2	0

Variants in LRRIQ4

This is a list of pathogenic ClinVar variants found in the LRRIQ4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-169821940-T-A		not specified	Uncertain significance (Sep 20, 2023)
3-169822116-G-C		not specified	Uncertain significance (May 14, 2024)
3-169822143-G-C		not specified	Uncertain significance (Mar 28, 2024)
3-169822147-C-T		not specified	Uncertain significance (Dec 09, 2023)
3-169822154-T-C		not specified	Uncertain significance (Nov 01, 2022)
3-169822159-A-G		not specified	Uncertain significance (Jun 22, 2021)
3-169822214-G-T		not specified	Uncertain significance (Dec 14, 2021)
3-169822228-T-C		not specified	Uncertain significance (May 01, 2024)
3-169822232-A-T		not specified	Uncertain significance (Jan 26, 2023)
3-169822282-C-A		not specified	Uncertain significance (Oct 25, 2022)
3-169822291-C-T		not specified	Uncertain significance (Feb 15, 2023)
3-169822345-C-T		not specified	Uncertain significance (Jan 26, 2022)
3-169822430-T-G		not specified	Uncertain significance (Jan 12, 2024)
3-169822442-G-A		not specified	Likely benign (Dec 21, 2022)
3-169822453-G-C		not specified	Uncertain significance (Jun 28, 2022)
3-169822462-C-T		not specified	Uncertain significance (Feb 03, 2022)
3-169822520-T-C		not specified	Uncertain significance (Jul 14, 2023)
3-169822526-C-G		not specified	Uncertain significance (Jun 29, 2022)
3-169822526-C-T		not specified	Likely benign (Jun 13, 2023)
3-169822543-G-A		not specified	Uncertain significance (Jul 09, 2021)
3-169822603-G-A		not specified	Uncertain significance (Sep 29, 2023)
3-169822645-T-C		not specified	Uncertain significance (Mar 12, 2024)
3-169822670-C-T		not specified	Uncertain significance (Dec 08, 2023)
3-169822684-G-C		not specified	Uncertain significance (Jan 16, 2024)
3-169822739-C-A		not specified	Uncertain significance (May 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRIQ4	protein_coding	protein_coding	ENST00000340806	5	15854

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.78e-7	0.666	124565	0	75	124640	0.000301

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.204	295	305	0.967	0.0000174	3641
Missense in Polyphen		99	95.337	1.0384		1259
Synonymous	1.17	120	137	0.873	0.00000855	1109
Loss of Function	1.17	13	18.4	0.707	8.60e-7	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000661	0.000658
Ashkenazi Jewish	0.00	0.00
East Asian	0.000614	0.000612
Finnish	0.000468	0.000464
European (Non-Finnish)	0.000134	0.000133
Middle Eastern	0.000614	0.000612
South Asian	0.000818	0.000817
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0988

Intolerance Scores

• loftool: 0.887
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.65

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.218

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrriq4