Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	11133
Gene name	Kaptin, actin binding protein
Gene symbol	KPTN
Synonyms (NCBI Gene)	2E4KICS4MRT41
Chromosome	19
Chromosome location	19q13.32
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

Show/Hide all (6)

SNP ID	Visualize variation	Clinical significance	Consequence
rs374298314	G>A,T	Pathogenic	Stop gained, genic downstream transcript variant, missense variant, non coding transcript variant, coding sequence variant
rs587777148	->GACCACATCTGCAGAACC	Pathogenic	Genic downstream transcript variant, coding sequence variant, non coding transcript variant, inframe insertion
rs761616995	G>A	Likely-pathogenic	Coding sequence variant, stop gained, non coding transcript variant, genic downstream transcript variant
rs766372684	->TA	Pathogenic	Frameshift variant, downstream transcript variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant, intron variant, splice donor variant
rs774473819	C>T	Likely-pathogenic	Intron variant, genic downstream transcript variant
rs1295123083	->T	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant, genic downstream transcript variant

Show/Hide all (21)

miRTarBase ID	miRNA	Experiments	Reference
MIRT049806	hsa-miR-92a-3p	CLASH	23622248
MIRT1100499	hsa-miR-3135b	CLIP-seq
MIRT1100500	hsa-miR-3150a-3p	CLIP-seq
MIRT1100501	hsa-miR-3175	CLIP-seq
MIRT1100502	hsa-miR-3620	CLIP-seq
MIRT1100503	hsa-miR-3652	CLIP-seq
MIRT1100504	hsa-miR-3663-3p	CLIP-seq
MIRT1100505	hsa-miR-3689d	CLIP-seq
MIRT1100506	hsa-miR-4292	CLIP-seq
MIRT1100507	hsa-miR-4430	CLIP-seq
MIRT1100508	hsa-miR-4667-5p	CLIP-seq
MIRT1100509	hsa-miR-4700-5p	CLIP-seq
MIRT1100510	hsa-miR-4792	CLIP-seq
MIRT1100511	hsa-miR-637	CLIP-seq
MIRT1100512	hsa-miR-939	CLIP-seq
MIRT2027367	hsa-miR-1197	CLIP-seq
MIRT2027368	hsa-miR-205	CLIP-seq
MIRT2027369	hsa-miR-4421	CLIP-seq
MIRT2027370	hsa-miR-4436a	CLIP-seq
MIRT1100501	hsa-miR-3175	CLIP-seq
MIRT1100501	hsa-miR-3175	CLIP-seq

Show/Hide all (30)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003779	Function	Actin binding	IEA
GO:0005515	Function	Protein binding	IPI	33961781, 38288086
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005765	Component	Lysosomal membrane	NAS	28199306
GO:0005765	Component	Lysosomal membrane	TAS
GO:0007015	Process	Actin filament organization	IEA
GO:0015629	Component	Actin cytoskeleton	IEA
GO:0016020	Component	Membrane	IEA
GO:0030027	Component	Lamellipodium	IBA
GO:0030027	Component	Lamellipodium	IDA	10099934, 24239382
GO:0030027	Component	Lamellipodium	IEA
GO:0031941	Component	Filamentous actin	IDA	24239382
GO:0032420	Component	Stereocilium	IEA
GO:0032420	Component	Stereocilium	ISS
GO:0034198	Process	Cellular response to amino acid starvation	IBA
GO:0034198	Process	Cellular response to amino acid starvation	IMP	28199306
GO:0042149	Process	Cellular response to glucose starvation	IMP	28199306
GO:0042995	Component	Cell projection	IEA
GO:0051015	Function	Actin filament binding	IBA
GO:0051015	Function	Actin filament binding	IDA	10099934
GO:0061462	Process	Protein localization to lysosome	IMP	28199306
GO:0098871	Component	Postsynaptic actin cytoskeleton	IDA	24239382
GO:0098871	Component	Postsynaptic actin cytoskeleton	IEA
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0140007	Component	KICSTOR complex	IBA
GO:0140007	Component	KICSTOR complex	IDA	28199306
GO:0140007	Component	KICSTOR complex	NAS	28199306
GO:1904262	Process	Negative regulation of TORC1 signaling	IBA
GO:1904262	Process	Negative regulation of TORC1 signaling	IMP	28199306

MIM	HGNC	e!Ensembl
615620	6404	ENSG00000118162

Q9Y664

Protein name

KICSTOR complex protein kaptin (Actin-associated protein 2E4)

Protein function

As part of the KICSTOR complex functions in the amino acid-sensing branch of the TORC1 signaling pathway. Recruits, in an amino acid-independent manner, the GATOR1 complex to the lysosomal membranes and allows its interaction with GATOR2 and the

Family and domains

Sequence

MMGEAAVAAGPCPLREDSFTRFSSQSNVYGLAGGAGGRGELLAATLKGKVLGFRYQDLRQ
KIRPVAKELQFNYIPVDAEIVSIDTFNKSPPKRGLVVGITFIKDSGDKGSPFLNIYCDYE
PGSEYNLDSIAQSCLNLELQFTPFQLCHAEVQVGDQLETVFLLSGNDPAIHLYKENEGLH
QFEEQPVENLFPELTNLTSSVLWLDVHNFPGTSRRLSALGCQSGYVRVAHVDQRSREVLQ
MWSVLQDGPISRVIVFSLSAAKETKDRPLQDEYSVLVASMLEPAVVYRDLLNRGLEDQLL
LPGSDQFDSVLCSLVTDVDLDGRPEVLVATYGQELLCYKYRGPESGLPEAQHGFHLLWQR
SFSSPLLAMAHVDLTGDGLQELAVVSLKGVHILQHSLIQASELVLTRLRHQVEQRRRRLQ
GLEDGAGAGPAENAAS

Sequence length

436

Interactions

View interactions

	Reactome
			Amino acids regulate mTORC1

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
KPTN-related disorder	Pathogenic; Likely pathogenic	rs374298314, rs587777148	RCV004755772 RCV003415870	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Macrocephaly-developmental delay syndrome	Likely pathogenic; Pathogenic	rs1192367520, rs374298314, rs587777148, rs1243527780, rs2122687472, rs2122670288, rs772378754, rs1967849812, rs2515242437, rs766372684, rs754861924, rs1967952850, rs1295123083	RCV001331685 RCV000087079 RCV000087080 RCV003745344 RCV001929790 View all (8 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
COMPLEX NEURODEVELOPMENTAL DISORDER	—	ClinGen, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 41	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (22)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Anxiety	Anxiety Disorder	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Class III malocclusion	Malocclusion	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Clinodactyly of the 5th finger	Camptodactyly of fingers	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Frontal bossing	Frontal bossing	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	25847626		★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	37311648	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypersensitivity Delayed	Hypersensitivity	Pubtator	24239382, 32358097	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	25847626		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	37311648	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Language Disorders	Language development disorders	Pubtator	37311648	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Macrocephaly	Macrocephaly	BEFREE	24239382, 25847626		★★★★★ ★☆☆☆☆ Found in Text Mining only
Macrocephaly	Macrocephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Macrocephaly-developmental delay syndrome	Macrocephaly-Developmental Delay Syndrome	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MENTAL RETARDATION, AUTOSOMAL RECESSIVE 41	Mental retardation	ORPHANET_DG	24239382		★★★★★ ★☆☆☆☆ Found in Text Mining only
MENTAL RETARDATION, AUTOSOMAL RECESSIVE 41	Mental retardation	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
MENTAL RETARDATION, AUTOSOMAL RECESSIVE 41	Mental retardation	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Movement Disorders	Movement disorder	Pubtator	37311648	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Scaphycephaly	Scaphocephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	24239382, 32358097	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stereotyped Behavior	Stereotyped Behavior	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

KPTN (kaptin, actin binding protein)