NCKAP1 NCK associated protein 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NCKAP1provided by HGNC
Official Full Name: NCK associated protein 1provided by HGNC
Primary source: HGNC:HGNC:7666
See related: Ensembl:ENSG00000061676 MIM:604891; AllianceGenome:HGNC:7666
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HEM2; NAP1; NAP125; p125Nap1
Summary: Contributes to small GTPase binding activity. Involved in Rac protein signal transduction; positive regulation of Arp2/3 complex-mediated actin nucleation; and positive regulation of lamellipodium assembly. Located in extracellular exosome and focal adhesion. Part of SCAR complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in thyroid (RPKM 62.7), brain (RPKM 61.6) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q32.1

Exon count:: 32

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (182909115..183038457, complement)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (183398094..183527479, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (183773843..183903185, complement)

Chromosome 2 - NC_000002.12 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
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?

Role of NCKAP1 in the Defective Phagocytic Function of Microglia-Like Cells Derived from Rapidly Progressing Sporadic ALS.
Title: Role of NCKAP1 in the Defective Phagocytic Function of Microglia-Like Cells Derived from Rapidly Progressing Sporadic ALS.
Circ_NCKAP1 promotes skin basal cell carcinoma progression by sponging the miR-148b-5p/HSP90 axis.
Title: Circ_NCKAP1 promotes skin basal cell carcinoma progression by sponging the miR-148b-5p/HSP90 axis.
NCKAP1 Disruptive Variants Lead to a Neurodevelopmental Disorder with Core Features of Autism.
Title: NCKAP1 Disruptive Variants Lead to a Neurodevelopmental Disorder with Core Features of Autism.
NCKAP1 is a tumor suppress gene that modulates the cell cycle of HCC cell lines by targeting Rb1/p53 regulation.
Title: NCKAP1 improves patient outcome and inhibits cell growth by enhancing Rb1/p53 activation in hepatocellular carcinoma.
Results demonstrate the importance and functional regulation of the HSP90-NAP1 protein complex in cancer metastatic signaling.
Title: Nck-associated protein 1 associates with HSP90 to drive metastasis in human non-small-cell lung cancer.
we show that stapled peptides targeting the interface between NCKAP1 and CYFIP1 destabilize the WASF3 complex... thereby suppressing invasion and metastasis of breast cancer cells.
Title: The WASF3-NCKAP1-CYFIP1 Complex Is Essential for Breast Cancer Metastasis.
We identify three mosaic missense and likely-gene disrupting mutations in genes previously implicated in ASD (KMT2C, NCKAP1, and MYH10) in probands but none in siblings. We find a strong ascertainment bias for mosaic mutations in probands relative to their unaffected siblings
Title: The Contribution of Mosaic Variants to Autism Spectrum Disorder.
miR-34c-3p functions as a tumor promoter by targeting NCKAP1 that is associated with prognosis in hepatocellular carcinoma.
Title: MicroRNA-34c-3p promotes cell proliferation and invasion in hepatocellular carcinoma by regulation of NCKAP1 expression.

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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

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2017-12-27) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2017-12-27) ClinGen Genome Curation PagePubMed

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
Knockdown of NCK-associated protein 1 (NCKAP1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Upregulation of apoptosis genes such as NCK-associated protein 1, PTB domain adaptor protein CED-6, and TNF receptor superfamily 5 are induced by HIV-1 gp120 in human neurons	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

D2S350 (e-PCR)
- UniSTS:75558

RH122355 (e-PCR)
- UniSTS:138309

D2S350 (e-PCR)
- UniSTS:61897

RH12037 (e-PCR)
- UniSTS:13008

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
contributes_to small GTPase binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in Rac protein signal transduction	IDA Inferred from Direct Assay more info	PubMed
involved_in apoptotic process	TAS Traceable Author Statement more info	PubMed
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in cell morphogenesis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in cell projection assembly	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in central nervous system development	TAS Traceable Author Statement more info	PubMed
involved_in cortical actin cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in neuron projection morphogenesis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of Arp2/3 complex-mediated actin nucleation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of actin filament polymerization	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of lamellipodium assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of lamellipodium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of lamellipodium assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of SCAR complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of SCAR complex	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
part_of filamentous actin	ISS Inferred from Sequence or Structural Similarity more info
located_in focal adhesion	HDA more info	PubMed
located_in lamellipodium	ISS Inferred from Sequence or Structural Similarity more info
located_in lamellipodium membrane	IEA Inferred from Electronic Annotation more info
located_in ruffle	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: nck-associated protein 1

Names: membrane-associated protein HEM-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.

mRNA and Protein(s)

NM_013436.5 → NP_038464.1 nck-associated protein 1 isoform 1

See identical proteins and their annotated locations for NP_038464.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).

Source sequence(s)

AB011159, AC108514, BC015025, CA314471

Consensus CDS

CCDS2287.1

UniProtKB/Swiss-Prot

O60329, Q53QN5, Q53S94, Q53Y35, Q9Y2A7

Related

ENSP00000355348.3, ENST00000361354.9

Conserved Domains (1) summary

pfam09735
Location:13 → 1122

Nckap1; Membrane-associated apoptosis protein
NM_205842.3 → NP_995314.1 nck-associated protein 1 isoform 2

See identical proteins and their annotated locations for NP_995314.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AB011159, AC108514, BC015025, CA314471

Consensus CDS

CCDS2288.1

UniProtKB/Swiss-Prot

Q9Y2A7

Related

ENSP00000354251.2, ENST00000360982.2

Conserved Domains (1) summary

pfam09735
Location:13 → 1128

Nckap1; Membrane-associated apoptosis protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

182909115..183038457 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006712201.4 → XP_006712264.1 nck-associated protein 1 isoform X2

See identical proteins and their annotated locations for XP_006712264.1

UniProtKB/TrEMBL

A0A994J4I5

Related

ENSP00000515490.1, ENST00000703825.1

Conserved Domains (1) summary

pfam09735
Location:13 → 1120

Nckap1; Membrane-associated apoptosis protein
XM_006712200.4 → XP_006712263.1 nck-associated protein 1 isoform X1

See identical proteins and their annotated locations for XP_006712263.1

UniProtKB/TrEMBL

A0A994J6K9

Related

ENSP00000515489.1, ENST00000703824.1

Conserved Domains (1) summary

pfam09735
Location:13 → 1126

Nckap1; Membrane-associated apoptosis protein

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

183398094..183527479 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054340221.1 → XP_054196196.1 nck-associated protein 1 isoform X2

UniProtKB/TrEMBL

A0A994J4I5
XM_054340220.1 → XP_054196195.1 nck-associated protein 1 isoform X1

UniProtKB/TrEMBL

A0A994J6K9