KIRREL2

kirre like nephrin family adhesion molecule 2, the group of I-set domain containing|C2-set domain containing

Basic information

Region (hg38): 19:35855860-35867136

Links

ENSG00000126259 ∙ NCBI:84063 ∙ OMIM:607762 ∙ HGNC:18816 ∙ Uniprot:Q6UWL6 ∙ 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 KIRREL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIRREL2 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			35	4	1	40
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	4	1

Variants in KIRREL2

This is a list of pathogenic ClinVar variants found in the KIRREL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35857131-G-A		not specified	Uncertain significance (May 30, 2023)
19-35857133-G-A		not specified	Uncertain significance (Feb 17, 2023)
19-35857153-C-G		not specified	Uncertain significance (Apr 17, 2024)
19-35857380-C-G		not specified	Uncertain significance (Jan 30, 2024)
19-35857462-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-35857471-T-C		not specified	Uncertain significance (Aug 03, 2022)
19-35858417-G-C		not specified	Uncertain significance (Feb 22, 2023)
19-35858440-G-C		not specified	Uncertain significance (Jul 20, 2021)
19-35858539-G-A			Uncertain significance (-)
19-35858767-C-G		not specified	Uncertain significance (Feb 28, 2024)
19-35858787-C-T		not specified	Uncertain significance (Dec 06, 2023)
19-35859511-G-A		not specified	Uncertain significance (Apr 24, 2024)
19-35859556-G-T		not specified	Uncertain significance (Dec 14, 2021)
19-35859572-G-A			Benign (Apr 19, 2018)
19-35859620-T-C		not specified	Uncertain significance (May 31, 2023)
19-35859626-T-C		not specified	Uncertain significance (Oct 02, 2023)
19-35860368-C-G		not specified	Uncertain significance (Feb 14, 2023)
19-35860628-G-T		not specified	Uncertain significance (Feb 16, 2023)
19-35860969-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-35860983-T-C		not specified	Uncertain significance (Dec 15, 2023)
19-35860986-C-T		not specified	Uncertain significance (May 25, 2022)
19-35861026-G-A		not specified	Uncertain significance (Aug 10, 2021)
19-35861126-T-C		not specified	Uncertain significance (Jan 23, 2024)
19-35861170-G-A		not specified	Uncertain significance (Aug 01, 2022)
19-35861182-T-A		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIRREL2	protein_coding	protein_coding	ENST00000360202	15	11249

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.81e-10	0.958	125307	2	439	125748	0.00176

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.605	392	427	0.918	0.0000238	4405
Missense in Polyphen		92	104.28	0.88223		1102
Synonymous	0.228	183	187	0.979	0.0000107	1596
Loss of Function	2.10	20	33.0	0.606	0.00000175	339

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00378	0.00376
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000327	0.000326
Finnish	0.000150	0.000139
European (Non-Finnish)	0.00263	0.00257
Middle Eastern	0.000327	0.000326
South Asian	0.000851	0.000850
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate basal insulin secretion. {ECO:0000250|UniProtKB:Q7TSU7}.
• Pathway: Primary Focal Segmental Glomerulosclerosis FSGS;Nephrin family interactions;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.895
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.7

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.120

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kirrel2
• Phenotype: normal phenotype

Gene ontology

• Biological process: negative regulation of protein phosphorylation;cell adhesion;cell-cell adhesion
• Cellular component: plasma membrane;cell-cell junction;integral component of membrane;slit diaphragm
• Molecular function: protein binding;identical protein binding