KCTD1 (potassium channel tetramerization domain containing 1)

Gene

• Entrez ID: 284252
• Gene name: Potassium channel tetramerization domain containing 1
• Gene symbol: KCTD1
• Synonyms (NCBI Gene): C18orf5
• Chromosome: 18
• Chromosome location: 18q11.2
• Summary: This gene encodes a protein containing a BTB (Broad-complex, tramtrack and bric a brac), also known as a POZ (POxvirus and zinc finger) protein-protein interaction domain. The encoded protein negatively regulates the AP-2 family of transcription factors a

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs587776998	G>A,T	Pathogenic	Coding sequence variant, missense variant
rs587776999	G>A,C,T	Pathogenic	Coding sequence variant, missense variant
rs587777000	G>A,T	Pathogenic	Synonymous variant, coding sequence variant, missense variant
rs587777001	T>G	Pathogenic	Coding sequence variant, missense variant
rs587777002	T>G	Pathogenic	Coding sequence variant, missense variant
rs587777003	C>T	Pathogenic	Coding sequence variant, missense variant
rs878853124	G>T	Pathogenic	Coding sequence variant, missense variant
rs878853125	G>A	Pathogenic	Coding sequence variant, missense variant
rs886041986	G>A	Pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT052617	hsa-let-7a-5p	CLASH	23622248
MIRT048196	hsa-miR-196a-5p	CLASH	23622248
MIRT1082718	hsa-miR-450b-5p	CLIP-seq
MIRT1082719	hsa-miR-4722-3p	CLIP-seq
MIRT1082720	hsa-miR-4762-3p	CLIP-seq
MIRT1082721	hsa-miR-1197	CLIP-seq
MIRT1082722	hsa-miR-29a	CLIP-seq
MIRT1082723	hsa-miR-29b	CLIP-seq
MIRT1082724	hsa-miR-29c	CLIP-seq
MIRT1082725	hsa-miR-3065-3p	CLIP-seq
MIRT1082726	hsa-miR-4436a	CLIP-seq
MIRT1082727	hsa-miR-4493	CLIP-seq
MIRT1082728	hsa-miR-4529-5p	CLIP-seq
MIRT2020660	hsa-miR-1294	CLIP-seq
MIRT2020661	hsa-miR-129-5p	CLIP-seq
MIRT2020662	hsa-miR-197	CLIP-seq
MIRT2020663	hsa-miR-23a	CLIP-seq
MIRT2020664	hsa-miR-23b	CLIP-seq
MIRT2020665	hsa-miR-23c	CLIP-seq
MIRT2020666	hsa-miR-3138	CLIP-seq
MIRT2020667	hsa-miR-3613-3p	CLIP-seq
MIRT2020668	hsa-miR-4316	CLIP-seq
MIRT2020669	hsa-miR-4677-3p	CLIP-seq
MIRT2020670	hsa-miR-4679	CLIP-seq
MIRT2020671	hsa-miR-561	CLIP-seq
MIRT1082721	hsa-miR-1197	CLIP-seq
MIRT2020661	hsa-miR-129-5p	CLIP-seq
MIRT2020662	hsa-miR-197	CLIP-seq
MIRT1082722	hsa-miR-29a	CLIP-seq
MIRT1082723	hsa-miR-29b	CLIP-seq
MIRT1082724	hsa-miR-29c	CLIP-seq
MIRT1082725	hsa-miR-3065-3p	CLIP-seq
MIRT2252336	hsa-miR-3173-3p	CLIP-seq
MIRT2252337	hsa-miR-3657	CLIP-seq
MIRT2252338	hsa-miR-3909	CLIP-seq
MIRT2252339	hsa-miR-4428	CLIP-seq
MIRT1082728	hsa-miR-4529-5p	CLIP-seq
MIRT2252340	hsa-miR-4669	CLIP-seq
MIRT2252341	hsa-miR-665	CLIP-seq
MIRT2252342	hsa-miR-892a	CLIP-seq
MIRT2555667	hsa-miR-1323	CLIP-seq
MIRT2555668	hsa-miR-182	CLIP-seq
MIRT2555669	hsa-miR-383	CLIP-seq
MIRT2555670	hsa-miR-4328	CLIP-seq
MIRT2555671	hsa-miR-4470	CLIP-seq
MIRT2555672	hsa-miR-4772-5p	CLIP-seq
MIRT2555673	hsa-miR-548a-3p	CLIP-seq
MIRT2555674	hsa-miR-548e	CLIP-seq
MIRT2555675	hsa-miR-548f	CLIP-seq
MIRT2555676	hsa-miR-548o	CLIP-seq
MIRT2555667	hsa-miR-1323	CLIP-seq
MIRT2555668	hsa-miR-182	CLIP-seq
MIRT2555669	hsa-miR-383	CLIP-seq
MIRT2555670	hsa-miR-4328	CLIP-seq
MIRT2555671	hsa-miR-4470	CLIP-seq
MIRT2555672	hsa-miR-4772-5p	CLIP-seq
MIRT2555673	hsa-miR-548a-3p	CLIP-seq
MIRT2555674	hsa-miR-548e	CLIP-seq
MIRT2555675	hsa-miR-548f	CLIP-seq
MIRT2555676	hsa-miR-548o	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003714	Function	Transcription corepressor activity	IBA
GO:0003714	Function	Transcription corepressor activity	IDA	19115315
GO:0005515	Function	Protein binding	IPI	25416956, 29892012, 31515488, 32296183, 38113115
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	19115315
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0008134	Function	Transcription factor binding	IPI	19115315
GO:0042802	Function	Identical protein binding	IEA
GO:0042802	Function	Identical protein binding	IPI	25416956, 27152988, 32296183
GO:0045892	Process	Negative regulation of DNA-templated transcription	IBA
GO:0045892	Process	Negative regulation of DNA-templated transcription	IDA	19115315
GO:0051260	Process	Protein homooligomerization	IEA

Other IDs

• MIM: 613420
• HGNC: 18249
• e!Ensembl: ENSG00000134504

Protein

• UniProt ID: Q719H9
• Protein name: BTB/POZ domain-containing protein KCTD1 (Potassium channel tetramerization domain-containing protein 1)
• Protein function: May repress the transcriptional activity of AP-2 family members, including TFAP2A, TFAP2B and TFAP2C to various extent.
• PDB: 5BXB, 5BXD, 6S4L
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02214	BTB_2	32 → 124	BTB/POZ domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed in mammary gland, kidney, brain and ovary. {ECO:0000269|PubMed:18358072}.
• Sequence:

  MSRPLITRSPASPLNNQGIPTPAQLTKSNAPVHIDVGGHMYTSSLATLTKYPESRIGRLF
  DGTEPIVLDSLKQHYFIDRDGQMFRYILNFLRTSKLLIPDDFKDYTLLYEEAKYFQLQPM
  LLEMERWKQDRETGRFSRPCECLVVRVAPDLGERITLSGDKSLIEEVFPEIGDVMCNSVN
  AGWNHDSTHVIRFPLNGYCHLNSVQVLERLQQRGFEIVGSCGGGVDSSQFSEYVLRRELR
  RTPRVPSVIRIKQEPLD

• Sequence length: 257

Pathways

Reactome:

Negative regulation of activity of TFAP2 (AP-2) family transcription factors

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Scalp-ear-nipple syndrome	Pathogenic; Likely pathogenic	rs878853124, rs878853125, rs2510943436, rs587776998, rs587776999, rs587777000, rs587777001, rs587777002, rs587777003	RCV000224280 RCV000224008 RCV004594860 RCV000049292 RCV000049293 RCV000049294 RCV000049295 RCV000049296 RCV000049297 RCV000049298 RCV000049299	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANDROGENETIC ALOPECIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTROCYTOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KCTD1-related disorder	Benign; Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULAR SARCOIDOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
2-3 toe syndactyly	Syndactyly Of The Toes	HPO_DG			★☆☆☆☆ Found in Text Mining only
3-4 finger cutaneous syndactyly	Syndactyly of fingers	HPO_DG			★☆☆☆☆ Found in Text Mining only
Anodontia of Permanent Dentition	Anodontia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Aplasia Cutis Congenita	Aplasia Cutis Congenita	BEFREE	23541344		★☆☆☆☆ Found in Text Mining only
Aplasia Cutis Congenita	Aplasia Cutis Congenita	HPO_DG			★☆☆☆☆ Found in Text Mining only
Branchio-Oculo-Facial Syndrome	Branchiooculofacial Syndrome	BEFREE	23541344		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	GWASCAT_DG	29059683		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cardiovascular Diseases	Cardiovascular Diseases	BEFREE	21658281		★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital absence of breast	Breast aplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital small ears	Microtia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Craniofacial Abnormalities	Craniofacial abnormalities	Pubtator	38296633	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	30864372		★☆☆☆☆ Found in Text Mining only
Diabetic Retinopathy	Diabetic retinopathy	Pubtator	38194422	Associate	★☆☆☆☆ Found in Text Mining only
Double ureter	Double Ureter	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ectodermal Dysplasia	Ectodermal dysplasia	Pubtator	23541344, 38296633	Associate	★☆☆☆☆ Found in Text Mining only
Heart Defects Congenital	Congenital heart defect	Pubtator	33000225	Associate	★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypohidrosis	Hypohidrosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
NAIL DISORDER, NONSYNDROMIC CONGENITAL, 9	Nail Diseases	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nail dysplasia	Nail dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pyelonephritis	Pyelonephritis	HPO_DG			★☆☆☆☆ Found in Text Mining only
SCALP-EAR-NIPPLE SYNDROME	Scalp-Ear-Nipple Syndrome	BEFREE	23541344, 28818080, 31324836		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SCALP-EAR-NIPPLE SYNDROME	Scalp-Ear-Nipple Syndrome	CLINVAR_DG	23541344		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SCALP-EAR-NIPPLE SYNDROME	Scalp-Ear-Nipple Syndrome	ORPHANET_DG	23541344		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SCALP-EAR-NIPPLE SYNDROME	Scalp-Ear-Nipple Syndrome	GENOMICS_ENGLAND_DG	23541344		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SCALP-EAR-NIPPLE SYNDROME	Scalp-Ear-Nipple Syndrome	UNIPROT_DG	23541344		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Scalp-ear-nipple syndrome	Scalp-Ear-Nipple Syndrome	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SCALP-EAR-NIPPLE SYNDROME	Scalp-Ear-Nipple Syndrome	CTD_human_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)