KPTN kaptin, actin binding protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: KPTNprovided by HGNC
Official Full Name: kaptin, actin binding proteinprovided by HGNC
Primary source: HGNC:HGNC:6404
See related: Ensembl:ENSG00000118162 MIM:615620; AllianceGenome:HGNC:6404
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: 2E4; KICS4; MRT41
Summary: This gene encodes a filamentous-actin-associated protein, which is involved in actin dynamics and plays an important role in neuromorphogenesis. This protein is part of the KICSTOR protein complex that localizes to lysosomes. Mutations in this gene result in an autosomal recessive form of intellectual disability. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2017]
Expression: Ubiquitous expression in bone marrow (RPKM 1.7), testis (RPKM 1.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.32

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (47475150..47485839, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (50306001..50316700, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (47978407..47987476, complement)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

Nonsense variant in a consanguineous family expands the phenotype of KPTN gene-related syndrome to include hearing impairment.
Title: Nonsense variant in a consanguineous family expands the phenotype of KPTN gene-related syndrome to include hearing impairment.
Pathogenic variants in KPTN, a rare cause of macrocephaly and intellectual disability.
Title: Pathogenic variants in KPTN, a rare cause of macrocephaly and intellectual disability.
Pathogenic variants in KPTN gene identified by clinical whole-genome sequencing.
Title: Pathogenic variants in KPTN gene identified by clinical whole-genome sequencing.
identification of a protein complex (KICSTOR) that is composed of four proteins, KPTN, ITFG2, C12orf66 and SZT2, and that is required for amino acid or glucose deprivation to inhibit mTORC1 in cultured human cells
Title: KICSTOR recruits GATOR1 to the lysosome and is necessary for nutrients to regulate mTORC1.
We have demonstrated that mutations in KPTN, encoding kaptin, cause a syndrome typified by macrocephaly, neurodevelopmental delay, and seizures.
Title: Mutations in KPTN cause macrocephaly, neurodevelopmental delay, and seizures.

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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
Macrocephaly-developmental delay syndrome MedGen: C3810225 OMIM: 615637 GeneReviews: KPTN-Related Disorder	Compare labs

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

KPTN (e-PCR)
- UniSTS:504433

SHGC-2349 (e-PCR)
- UniSTS:23704

STS-Z41308 (e-PCR)
- UniSTS:58319

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actin filament binding	IBA Inferred from Biological aspect of Ancestor more info
enables actin filament binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in actin filament organization	IEA Inferred from Electronic Annotation more info
involved_in cellular response to amino acid starvation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to amino acid starvation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to glucose starvation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of TORC1 signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of TORC1 signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to lysosome	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of KICSTOR complex	IBA Inferred from Biological aspect of Ancestor more info
part_of KICSTOR complex	IDA Inferred from Direct Assay more info	PubMed
part_of KICSTOR complex	NAS Non-traceable Author Statement more info	PubMed
part_of filamentous actin	IDA Inferred from Direct Assay more info	PubMed
is_active_in lamellipodium	IBA Inferred from Biological aspect of Ancestor more info
located_in lamellipodium	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	NAS Non-traceable Author Statement more info	PubMed
located_in lysosomal membrane	TAS Traceable Author Statement more info
located_in postsynaptic actin cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
located_in stereocilium	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: KICSTOR complex protein kaptin

Names: actin-associated protein 2E4; epididymis secretory sperm binding protein

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_034097.1 RefSeqGene

Range

5046..14115

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001291296.2 → NP_001278225.1 KICSTOR complex protein kaptin isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks two consecutive exons in the 5' coding region, but maintains the reading frame, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.

Source sequence(s)

AK298672, BG388698, DA129265, DR759729

UniProtKB/Swiss-Prot

Q9Y664

Conserved Domains (1) summary

pfam13517
Location:261 → 328

VCBS; Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
NM_007059.4 → NP_008990.2 KICSTOR complex protein kaptin isoform 1

See identical proteins and their annotated locations for NP_008990.2

Status: REVIEWED

Description

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

Source sequence(s)

AF105369, AK023996, AK225419, DA129265

Consensus CDS

CCDS42583.1

UniProtKB/Swiss-Prot

B3KN86, B4DQ76, Q96GT1, Q9Y664

UniProtKB/TrEMBL

A0A384NLB4

Related

ENSP00000337850.2, ENST00000338134.8

Conserved Domains (1) summary

pfam13517
Location:317 → 384

VCBS; Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella

RNA

NR_111923.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an additional segment and an additional exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF105369, AK298672, BG388698, DA129265

Related

ENST00000594208.5

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_000019.10 Reference GRCh38.p14 Primary Assembly

Range

47475150..47485839 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017026228.2 → XP_016881717.1 KICSTOR complex protein kaptin isoform X2
XM_017026227.2 → XP_016881716.1 KICSTOR complex protein kaptin isoform X1
XM_024451333.2 → XP_024307101.1 KICSTOR complex protein kaptin isoform X3

Conserved Domains (1) summary

pfam13517
Location:317 → 384

VCBS; Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella