KIRREL3 kirre like nephrin family adhesion molecule 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: KIRREL3provided by HGNC
Official Full Name: kirre like nephrin family adhesion molecule 3provided by HGNC
Primary source: HGNC:HGNC:23204
See related: Ensembl:ENSG00000149571 MIM:607761; AllianceGenome:HGNC:23204
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MRD4; KIRRE; NEPH2; PRO4502
Summary: The protein encoded by this gene is a member of the nephrin-like protein family. These proteins are expressed in fetal and adult brain, and also in podocytes of kidney glomeruli. The cytoplasmic domains of these proteins interact with the C-terminus of podocin, also expressed in the podocytes, cells involved in ensuring size- and charge-selective ultrafiltration. The protein encoded by this gene is a synaptic cell adhesion molecule with multiple extracellular immunoglobulin-like domains and a cytoplasmic PDZ domain-binding motif. Mutations in this gene are associated with several neurological and cognitive disorders. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]
Expression: Biased expression in brain (RPKM 6.0), adrenal (RPKM 0.5) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 11q24.2

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (126423358..127000870, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (126454803..127036590, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (126293253..126870766, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Modular Splicing Is Linked to Evolution in the Synapse-Specificity Molecule Kirrel3.
Title: Modular Splicing Is Linked to Evolution in the Synapse-Specificity Molecule Kirrel3.
Preliminary study on the role and mechanism of KIRREL3 in the development of esophageal squamous cell carcinoma.
Title: Preliminary study on the role and mechanism of KIRREL3 in the development of esophageal squamous cell carcinoma.
KIRREL3 interacting proteins MAP1B and MYO16 are potential candidates for intellectual disability and autism spectrum disorder.
Title: Autism and Intellectual Disability-Associated KIRREL3 Interacts with Neuronal Proteins MAP1B and MYO16 with Potential Roles in Neurodevelopment.
Results presented demonstrate for the first time that there are at least 3 splice variants of Kirrel3 expressed in adult human skeletal muscle, two of which have never previously been identified in human muscle.
Title: Identification of novel Kirrel3 gene splice variants in adult human skeletal muscle.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study of gene-disease association. (HuGE Navigator)
Title: New genetic associations detected in a host response study to hepatitis B vaccine.
Alterations in KIRREL3 in patients with mild to severe intellectual disability are reported.
Title: Alterations in CDH15 and KIRREL3 in patients with mild to severe intellectual disability.

Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study identifies protein quantitative trait loci (pQTLs). EBI GWAS Catalog EBI GWAS CatalogPubMed
Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic variants associated with breast size also influence breast cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome wide association study of age at menarche in the Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs. EBI GWAS Catalog EBI GWAS CatalogPubMed
Web-based, participant-driven studies yield novel genetic associations for common traits. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S570 (e-PCR)
- UniSTS:89103

D11S4013 (e-PCR)
- UniSTS:76566

WI-12535 (e-PCR)
- UniSTS:66601

RH16279 (e-PCR)
- UniSTS:67124

RH47697 (e-PCR)
- UniSTS:3902

G31042 (e-PCR)
- UniSTS:55617

SHGC-144698 (e-PCR)
- UniSTS:172363

RH120460 (e-PCR)
- UniSTS:133455

D11S2675 (e-PCR)
- UniSTS:151901

SHGC-155432 (e-PCR)
- UniSTS:185193

A005M34 (e-PCR)
- UniSTS:18794

RH91997 (e-PCR)
- UniSTS:89195

D10S16 (e-PCR)
- UniSTS:155756

D4S3192 (e-PCR)
- UniSTS:40556

G32242 (e-PCR)
- UniSTS:116845

D15S1477 (e-PCR)
- UniSTS:474482

D11S2594 (e-PCR)
- UniSTS:9588

D11S1119 (e-PCR)
- UniSTS:55688

D11S3229 (e-PCR)
- UniSTS:152474

D11S430 (e-PCR)
- UniSTS:148125

G59560 (e-PCR)
- UniSTS:136864

SHGC-143515 (e-PCR)
- UniSTS:171940

SHGC-34972 (e-PCR)
- UniSTS:31913

D11S477 (e-PCR)
- UniSTS:148139

SHGC-144515 (e-PCR)
- UniSTS:174263

SHGC-31257 (e-PCR)
- UniSTS:37562

SHGC-106162 (e-PCR)
- UniSTS:169670

D11S1863 (e-PCR)
- UniSTS:148938

D11S3281 (e-PCR)
- UniSTS:152524

G59492 (e-PCR)
- UniSTS:136656

D11S2562 (e-PCR)
- UniSTS:79063

D11S3302 (e-PCR)
- UniSTS:152544

SHGC-82464 (e-PCR)
- UniSTS:104432

SHGC-146231 (e-PCR)
- UniSTS:175092

D11S3857 (e-PCR)
- UniSTS:153080

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cell adhesion molecule binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell-cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in glomerulus morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in hemopoiesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in hippocampus development	ISS Inferred from Sequence or Structural Similarity more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	ISS Inferred from Sequence or Structural Similarity more info
involved_in inter-male aggressive behavior	IEA Inferred from Electronic Annotation more info
involved_in neuron migration	IEA Inferred from Electronic Annotation more info
involved_in neuron projection morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in principal sensory nucleus of trigeminal nerve development	IEA Inferred from Electronic Annotation more info
involved_in synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in synapse assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in axon	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cell-cell junction	IBA Inferred from Biological aspect of Ancestor more info
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic shaft	IEA Inferred from Electronic Annotation more info
located_in extracellular region	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: kin of IRRE-like protein 3

Names: kin of IRRE like 3; kin of irregular chiasm-like protein 3; nephrin-like 2; nephrin-like protein 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_012971.2 RefSeqGene

Range

5100..582512

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001161707.1 → NP_001155179.1 kin of IRRE-like protein 3 isoform 2 precursor

See identical proteins and their annotated locations for NP_001155179.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) includes an alternate segment at the 3' end compared to variant 1. This results in a frame-shift, and a shorter isoform (2) with a distinct C-terminus compared to isoform 1.

Source sequence(s)

AY358743, BC065255

Consensus CDS

CCDS55796.1

UniProtKB/Swiss-Prot

Q8IZU9

Related

ENSP00000435094.2, ENST00000525704.2

Conserved Domains (7) summary

cd05759
Location:165 → 246

Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)

cd05898
Location:418 → 515

Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)

smart00408
Location:349 → 400

IGc2; Immunoglobulin C-2 Type

smart00410
Location:426 → 515

IG_like; Immunoglobulin like

pfam07679
Location:335 → 416

I-set; Immunoglobulin I-set domain

pfam13895
Location:254 → 331

Ig_2; Immunoglobulin domain

cl11960
Location:52 → 143

Ig; Immunoglobulin domain
NM_001301097.1 → NP_001288026.1 kin of IRRE-like protein 3 isoform 3 precursor

See identical proteins and their annotated locations for NP_001288026.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AP000806, BC042432, BC065255, BM671831

Consensus CDS

CCDS73413.1

UniProtKB/TrEMBL

E9PRX9

Related

ENSP00000434081.2, ENST00000529097.6

Conserved Domains (7) summary

cd05759
Location:165 → 246

Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)

cd05898
Location:418 → 515

Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)

smart00408
Location:349 → 400

IGc2; Immunoglobulin C-2 Type

smart00410
Location:426 → 515

IG_like; Immunoglobulin like

pfam07679
Location:335 → 416

I-set; Immunoglobulin I-set domain

pfam13895
Location:254 → 331

Ig_2; Immunoglobulin domain

cl11960
Location:52 → 143

Ig; Immunoglobulin domain
NM_032531.4 → NP_115920.1 kin of IRRE-like protein 3 isoform 1 precursor

See identical proteins and their annotated locations for NP_115920.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AB058770, AP000806, AY358760, BC065255, BC101801, BM671831, W75978

Consensus CDS

CCDS53723.1

UniProtKB/Swiss-Prot

Q3MIJ7, Q6UWJ9, Q6UWL5, Q8IZU9, Q96JG0

Related

ENSP00000435466.2, ENST00000525144.7

Conserved Domains (7) summary

cd05759
Location:165 → 246

Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)

cd05898
Location:418 → 515

Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)

smart00408
Location:349 → 400

IGc2; Immunoglobulin C-2 Type

smart00410
Location:426 → 515

IG_like; Immunoglobulin like

pfam07679
Location:335 → 416

I-set; Immunoglobulin I-set domain

pfam13895
Location:254 → 331

Ig_2; Immunoglobulin domain

cl11960
Location:52 → 143

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

126423358..127000870 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017018419.2 → XP_016873908.1 kin of IRRE-like protein 3 isoform X3
XM_011543027.3 → XP_011541329.1 kin of IRRE-like protein 3 isoform X2

See identical proteins and their annotated locations for XP_011541329.1

Conserved Domains (7) summary

cd05759
Location:165 → 246

Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)

cd05898
Location:418 → 515

Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)

smart00408
Location:349 → 400

IGc2; Immunoglobulin C-2 Type

smart00410
Location:426 → 515

IG_like; Immunoglobulin like

pfam07679
Location:335 → 416

I-set; Immunoglobulin I-set domain

pfam13895
Location:254 → 331

Ig_2; Immunoglobulin domain

cl11960
Location:52 → 143

Ig; Immunoglobulin domain
XM_011543026.3 → XP_011541328.1 kin of IRRE-like protein 3 isoform X1

Conserved Domains (7) summary

cd05759
Location:171 → 252

Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)

cd05898
Location:424 → 521

Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)

smart00408
Location:355 → 406

IGc2; Immunoglobulin C-2 Type

smart00410
Location:432 → 521

IG_like; Immunoglobulin like

pfam07679
Location:341 → 422

I-set; Immunoglobulin I-set domain

pfam13895
Location:260 → 337

Ig_2; Immunoglobulin domain

cl11960
Location:58 → 149

Ig; Immunoglobulin domain
XM_011543032.4 → XP_011541334.1 kin of IRRE-like protein 3 isoform X5

Conserved Domains (7) summary

cd05759
Location:171 → 252

Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)

cd05898
Location:424 → 521

Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)

smart00408
Location:355 → 406

IGc2; Immunoglobulin C-2 Type

smart00410
Location:432 → 521

IG_like; Immunoglobulin like

pfam07679
Location:341 → 422

I-set; Immunoglobulin I-set domain

pfam13895
Location:260 → 337

Ig_2; Immunoglobulin domain

cl11960
Location:58 → 149

Ig; Immunoglobulin domain
XM_011543030.4 → XP_011541332.1 kin of IRRE-like protein 3 isoform X4

Conserved Domains (7) summary

cd05759
Location:171 → 252

Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)

cd05898
Location:424 → 521

Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)

smart00408
Location:355 → 406

IGc2; Immunoglobulin C-2 Type

smart00410
Location:432 → 521

IG_like; Immunoglobulin like

pfam07679
Location:341 → 422

I-set; Immunoglobulin I-set domain

pfam13895
Location:260 → 337

Ig_2; Immunoglobulin domain

cl11960
Location:58 → 149

Ig; Immunoglobulin domain
XM_047427715.1 → XP_047283671.1 kin of IRRE-like protein 3 isoform X6

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

126454803..127036590 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054370202.1 → XP_054226177.1 kin of IRRE-like protein 3 isoform X8

UniProtKB/TrEMBL

E9PRX9
XM_054370197.1 → XP_054226172.1 kin of IRRE-like protein 3 isoform X3
XM_054370199.1 → XP_054226174.1 kin of IRRE-like protein 3 isoform X7

UniProtKB/Swiss-Prot

Q3MIJ7, Q6UWJ9, Q6UWL5, Q8IZU9, Q96JG0
XM_054370195.1 → XP_054226170.1 kin of IRRE-like protein 3 isoform X2
XM_054370200.1 → XP_054226175.1 kin of IRRE-like protein 3 isoform X7

UniProtKB/Swiss-Prot

Q3MIJ7, Q6UWJ9, Q6UWL5, Q8IZU9, Q96JG0
XM_054370196.1 → XP_054226171.1 kin of IRRE-like protein 3 isoform X2
XM_054370194.1 → XP_054226169.1 kin of IRRE-like protein 3 isoform X1
XM_054370201.1 → XP_054226176.1 kin of IRRE-like protein 3 isoform X5
XM_054370198.1 → XP_054226173.1 kin of IRRE-like protein 3 isoform X4
XM_054370203.1 → XP_054226178.1 kin of IRRE-like protein 3 isoform X6