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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	154288
Gene name	KH domain containing 3 like, subcortical maternal complex member
Gene symbol	KHDC3L
Synonyms (NCBI Gene)	C6orf221ECAT1HYDM2
Chromosome	6
Chromosome location	6q13
Summary	The protein encoded by this gene belongs to the KHDC1 family, members of which contain an atypical KH domain that may not bind RNA like canonical KH domains. This gene is specifically expressed in the oocytes, and recent studies suggest that it may functi

Show/Hide all (5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs606231233	G>T	Pathogenic	Initiator codon variant, missense variant
rs606231234	GACT>-	Pathogenic	Frameshift variant, coding sequence variant
rs606231235	A>G	Pathogenic	Initiator codon variant, missense variant
rs606231286	TCAA>-	Pathogenic	Frameshift variant, coding sequence variant
rs745776920	C>T	Likely-pathogenic	Stop gained, coding sequence variant

Show/Hide all (1)

miRTarBase ID	miRNA	Experiments	Reference
MIRT018684	hsa-miR-335-5p	Microarray	18185580

Show/Hide all (34)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	25542835, 26537248, 31609975, 32296183
GO:0005634	Component	Nucleus	IDA	25542835, 31609975
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS
GO:0005694	Component	Chromosome	IEA
GO:0005737	Component	Cytoplasm	IDA	25542835
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	ISS
GO:0005813	Component	Centrosome	IEA
GO:0005813	Component	Centrosome	ISS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005938	Component	Cell cortex	IEA
GO:0005938	Component	Cell cortex	ISS
GO:0007015	Process	Actin filament organization	ISS
GO:0031297	Process	Replication fork processing	ISS
GO:0032880	Process	Regulation of protein localization	IMP	31609975
GO:0032880	Process	Regulation of protein localization	ISS
GO:0032991	Component	Protein-containing complex	IBA
GO:0032991	Component	Protein-containing complex	IDA	26537248
GO:0040019	Process	Positive regulation of embryonic development	ISS
GO:0043066	Process	Negative regulation of apoptotic process	ISS
GO:0050769	Process	Positive regulation of neurogenesis	ISS
GO:0051656	Process	Establishment of organelle localization	ISS
GO:0106333	Component	Subcortical maternal complex	IDA	25542835, 26537248
GO:0140089	Process	Protein storage	ISS
GO:0140094	Function	Structural constituent of cytoplasmic lattice	ISS
GO:0140095	Component	Cytoplasmic lattice	ISS
GO:1900006	Process	Positive regulation of dendrite development	ISS
GO:1905168	Process	Positive regulation of double-strand break repair via homologous recombination	IMP	31609975
GO:1905168	Process	Positive regulation of double-strand break repair via homologous recombination	ISS
GO:2000781	Process	Positive regulation of double-strand break repair	IEA
GO:2000781	Process	Positive regulation of double-strand break repair	ISS

MIM	HGNC	e!Ensembl
611687	33699	ENSG00000203908

Q587J8

Protein name

KH domain-containing protein 3 (ES cell-associated transcript 1 protein) (KHDC3-like protein)

Protein function

Component of the subcortical maternal complex (SCMC), a multiprotein complex that plays a key role in early embryonic development (By similarity). The SCMC complex is a structural constituent of cytoplasmic lattices, which consist in fibrous str

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF16005	MOEP19	29 → 114	KH-like RNA-binding domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expression appears to be maximal in germinal vesicle oocytes, it tails off through metaphase II oocytes and is undetectable following the completion of the oocyte to embryo transition. {ECO:0000269|PubMed:21885028}.

Sequence

MDAPRRFPTLVQLMQPKAMPVEVLGHLPKRFSWFHSEFLKNPKVVRLEVWLVEKIFGRGG
ERIPHVQGMSQILIHVNRLDPNGEAEILVFGRPSYQEDTIKMIMNLADYHRQLQAKGSGK
ALAQDVATQKAETQRSSIEVREAGTQRSVEVREAGTQRSVEVQEVGTQGSPVEVQEAGTQ
QSLQAANKSGTQRSPEAASKAVTQRFREDARDPVTRL

Sequence length

217

Interactions

View interactions

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
Hydatidiform mole, recurrent, 2	Pathogenic; Likely pathogenic	rs606231286, rs745776920, rs606231233, rs606231234	RCV000144944 RCV000190600 RCV000023914 RCV000023915	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
KHDC3L-related condition	Pathogenic	rs606231234	RCV004758598	★★★★★ ★★★★☆ 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.
COMPLETE HYDATIDIFORM MOLE	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hydatidiform mole	Benign	ClinVar CTD	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
PARTIAL HYDATIDIFORM MOLE	—	Orphanet	★★★★★ ★★☆☆☆ 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
Carcinoma Embryonal	Embryonal carcinoma	Pubtator	35946397	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Complete hydatidiform mole	Complete Hydatidiform Mole	ORPHANET_DG	21885028, 24533231		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Complete hydatidiform mole	Complete Hydatidiform Mole	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Complete hydatidiform mole	Complete Hydatidiform Mole	BEFREE	23125094, 23515668		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Complete hydatidiform mole	Complete Hydatidiform Mole	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	35946397	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Gestational Trophoblastic Disease	Gestational trophoblastic disease	Pubtator	30235719	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Gestational Trophoblastic Neoplasms	Gestational Trophoblastic Neoplasms	BEFREE	30235719		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hydatidiform Mole	Hydatidiform Mole	BEFREE	21885028, 22909446, 23515668, 23963444, 24105752, 24215781, 25358348, 25376457, 29458875, 31220306, 31847873		★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Hydatidiform Mole	Hydatidiform mole	Pubtator	21885028	Stimulate	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Hydatidiform Mole	Hydatidiform mole	Pubtator	23232697, 25376457, 29463882, 29693651, 31847873, 32592075, 34608573, 35361411, 36001209	Associate	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Hydatidiform Mole	Hydatidiform Mole	CTD_human_DG			★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Hydatidiform Mole	Hydatidiform Mole	HPO_DG			★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Hydatidiform Mole, Partial	Hydatidiform Mole	ORPHANET_DG	24533231		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hydatidiform Mole, Partial	Hydatidiform Mole	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
HYDATIDIFORM MOLE, RECURRENT, 1	Hydatidiform Mole	BEFREE	21885028, 24215781, 31847873		★★★★★ ★☆☆☆☆ Found in Text Mining only
HYDATIDIFORM MOLE, RECURRENT, 2	Hydatidiform Mole	CLINVAR_DG	21885028, 23232697		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Melanocytic nevus	Melanocytic nevus	BEFREE	26554776, 31220306		★★★★★ ★☆☆☆☆ Found in Text Mining only
Miscarriage	Miscarriage	BEFREE	23515668, 23963444		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nevus	Nevus	BEFREE	26554776, 31220306		★★★★★ ★☆☆☆☆ Found in Text Mining only
Partial hydatidiform mole	Partial Hydatidiform Mole	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pseudohypoparathyroidism Type 1B	Pseudohypoparathyroidism	Pubtator	35643636	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

KHDC3L (KH domain containing 3 like, subcortical maternal complex member)