KIRREL1

kirre like nephrin family adhesion molecule 1, the group of C2-set domain containing|I-set domain containing

Basic information

Region (hg38): 1:157993273-158100262

Previous symbols: [ "KIRREL" ]

Links

ENSG00000183853 ∙ NCBI:55243 ∙ OMIM:607428 ∙ HGNC:15734 ∙ Uniprot:Q96J84 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nephrotic syndrome, type 23 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephrotic syndrome, type 23	AR	Renal	Individuals have been described with early-onset nephrotic syndrome, with remission achieved through medical management	Renal	31472902

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIRREL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIRREL1 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			74			74
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		1	3
Total	0	0	76	0	1

Variants in KIRREL1

This is a list of pathogenic ClinVar variants found in the KIRREL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-157993680-C-G		not specified	Uncertain significance (Aug 02, 2023)
1-157993701-C-G		not specified	Uncertain significance (Jan 08, 2024)
1-157993705-C-A		not specified	Uncertain significance (Dec 07, 2023)
1-158076122-C-T		KIRREL1-related disorder	Benign (Dec 23, 2019)
1-158076124-C-T		not specified	Uncertain significance (Oct 14, 2021)
1-158076152-C-T		not specified	Uncertain significance (Jan 17, 2024)
1-158076170-G-A		not specified	Uncertain significance (Feb 10, 2025)
1-158076175-G-A		not specified • KIRREL1-related disorder	Benign (Mar 26, 2020)
1-158076236-C-T		not specified	Uncertain significance (Mar 20, 2024)
1-158076244-A-G		not specified	Uncertain significance (Dec 28, 2024)
1-158078000-G-A		not specified	Uncertain significance (Nov 24, 2024)
1-158078006-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-158078020-G-A		KIRREL1-related disorder	Likely benign (Dec 20, 2022)
1-158078026-G-A		KIRREL1-related disorder	Benign (Dec 18, 2019)
1-158078049-C-G		not specified	Uncertain significance (Sep 14, 2022)
1-158078104-G-A		not specified	Uncertain significance (Aug 27, 2024)
1-158078117-G-A		KIRREL1-related disorder • not specified	Uncertain significance (Jun 12, 2023)
1-158078119-C-T		not specified	Uncertain significance (Apr 01, 2024)
1-158078120-G-A		not specified	Uncertain significance (Oct 29, 2024)
1-158078126-A-G		not specified	Uncertain significance (Apr 04, 2023)
1-158084433-G-C		not specified	Uncertain significance (Jun 06, 2023)
1-158084447-C-T		KIRREL1-related disorder	Benign (Jan 28, 2020)
1-158084451-G-A		not specified	Uncertain significance (Nov 09, 2024)
1-158084479-C-A		not specified	Uncertain significance (Dec 11, 2023)
1-158084484-C-A		not specified	Uncertain significance (Jul 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIRREL1	protein_coding	protein_coding	ENST00000359209	15	106990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00145	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.61	333	496	0.671	0.0000322	4878
Missense in Polyphen		102	171.65	0.59422		1664
Synonymous	0.150	199	202	0.987	0.0000134	1601
Loss of Function	5.00	4	36.7	0.109	0.00000203	381

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a significant role in the normal development and function of the glomerular permeability. Signaling protein that needs the presence of TEC kinases to fully trans-activate the transcription factor AP-1 (By similarity). {ECO:0000250}.
• Pathway: TCR;EGFR1;Nephrin family interactions;Cell-Cell communication;Nephrin/Neph1 signaling in the kidney podocyte (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.14

Haploinsufficiency Scores

• pHI: 0.303
• hipred: Y
• hipred_score: 0.809
• ghis: 0.641

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Kirrel
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: kirrel1b
• Affected structure: podocyte
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: negative regulation of protein phosphorylation;excretion;positive regulation of actin filament polymerization;cell-cell adhesion
• Cellular component: plasma membrane;cell-cell junction;integral component of membrane;cell projection membrane;dendritic shaft;membrane raft;perinuclear region of cytoplasm
• Molecular function: protein binding;myosin binding