NCKAP1L NCK associated protein 1 like [Homo sapiens (human)] - Gene

Summary

Official Symbol: NCKAP1Lprovided by HGNC
Official Full Name: NCK associated protein 1 likeprovided by HGNC
Primary source: HGNC:HGNC:4862
See related: Ensembl:ENSG00000123338 MIM:141180; AllianceGenome:HGNC:4862
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: HEM1; IMD72
Summary: This gene encodes a member of the HEM family of tissue-specific transmembrane proteins which are highly conserved from invertebrates through mammals. This gene is only expressed in hematopoietic cells. The encoded protein is a part of the Scar/WAVE complex which plays an important role in regulating cell shape in both metazoans and plants. Alternatively spliced transcript variants encoding different isoforms have been found.[provided by RefSeq, May 2010]
Expression: Broad expression in lymph node (RPKM 38.4), appendix (RPKM 34.7) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q13.13-q13.2

Exon count:: 32

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (54497752..54548243)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (54464313..54514824)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (54891536..54942027)

Chromosome 12 - NC_000012.12 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 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?

Potential predictive value of immune-related genes FUCA1 and NCKAP1L for osteosarcoma metastasis.
Title: Potential predictive value of immune-related genes FUCA1 and NCKAP1L for osteosarcoma metastasis.
HEM1 Actin Immunodysregulatory Disorder: Genotypes, Phenotypes, and Future Directions.
Title: HEM1 Actin Immunodysregulatory Disorder: Genotypes, Phenotypes, and Future Directions.
Long non-coding RNA PVT1/microRNA miR-3127-5p/NCK-associated protein 1-like axis participates in the pathogenesis of abdominal aortic aneurysm by regulating vascular smooth muscle cells.
Title: Long non-coding RNA PVT1/microRNA miR-3127-5p/NCK-associated protein 1-like axis participates in the pathogenesis of abdominal aortic aneurysm by regulating vascular smooth muscle cells.
Prognostic Value of DNA Methylation-Driven Genes in Clear Cell Renal Cell Carcinoma: A Study Based on Methylation and Transcriptome Analyses.
Title: Prognostic Value of DNA Methylation-Driven Genes in Clear Cell Renal Cell Carcinoma: A Study Based on Methylation and Transcriptome Analyses.
NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation.
Title: NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation.
the evolutionarily conserved HEM1 protein simultaneously regulates filamentous actin (F-actin) and mTORC2 signaling to achieve equipoise in immune responses.
Title: HEM1 deficiency disrupts mTORC2 and F-actin control in inherited immunodysregulatory disease.
the Hem-1/Nap1 component of the Scar/WAVE complex localizes to propagating waves that appear to organize the leading edge of a motile neutrophil
Title: An actin-based wave generator organizes cell motility.
versatile Hem-1-containing complexes coordinate diverse regulatory signals at the leading edge of polarized neutrophils, including but not confined to those involving Verprolin-homologous protein-dependent actin polymerization
Title: Hem-1 complexes are essential for Rac activation, actin polymerization, and myosin regulation during neutrophil chemotaxis.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Immunodeficiency 72 with autoinflammation MedGen: C5436540 OMIM: 618982 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. 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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of NCKAP1L	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-H47633 (e-PCR)
- UniSTS:68164

SHGC-12875 (e-PCR)
- UniSTS:51698

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase activator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables TORC2 complex binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase activator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in B cell homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in B cell receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in T cell homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in actin polymerization-dependent cell motility	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell projection assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in cortical actin cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in cortical actin cytoskeleton organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cortical actin cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in erythrocyte development	IEP Inferred from Expression Pattern more info	PubMed
involved_in erythrocyte homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in maintenance of cell polarity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in myeloid cell homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cytotoxic T cell degranulation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of interleukin-17 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of interleukin-6 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron projection morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in neutrophil chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of B cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of B cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of CD4-positive, alpha-beta T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of CD8-positive, alpha-beta T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of T cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of T cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of TORC2 signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of actin filament polymerization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell adhesion mediated by integrin	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of erythrocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of gamma-delta T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of leukocyte migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of lymphocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of neutrophil chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of neutrophil migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of phagocytosis, engulfment	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein-containing complex assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to xenobiotic stimulus	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of SCAR complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SCAR complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in ficolin-1-rich granule membrane	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in secretory granule membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: nck-associated protein 1-like

Names: hematopoietic protein 1; membrane-associated protein hem-1

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.

mRNA and Protein(s)

NM_001184976.2 → NP_001171905.1 nck-associated protein 1-like isoform 2

See identical proteins and their annotated locations for NP_001171905.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an alternate 5' exon, resulting in a downstream in-frame AUG start codon, as compared to variant 1. The resulting isoform (2) has a shorter N-terminus, as compared to isoform 1.

Source sequence(s)

AC068789, AC079313, AK300783, AW575485

Consensus CDS

CCDS53799.1

UniProtKB/TrEMBL

Q9BV52

Related

ENSP00000445596.2, ENST00000545638.2

Conserved Domains (1) summary

pfam09735
Location:1 → 1073

Nckap1; Membrane-associated apoptosis protein
NM_005337.5 → NP_005328.2 nck-associated protein 1-like isoform 1

See identical proteins and their annotated locations for NP_005328.2

Status: REVIEWED

Description

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

Source sequence(s)

AC068789, AW575485, BC093769, BC093771, DA820115, M58285

Consensus CDS

CCDS31813.1

UniProtKB/Swiss-Prot

B4DUT5, P55160, Q52LW0

Related

ENSP00000293373.6, ENST00000293373.11

Conserved Domains (1) summary

pfam09735
Location:11 → 1123

Nckap1; Membrane-associated apoptosis protein