KHDC3L

KH domain containing 3 like, subcortical maternal complex member, the group of Subcortical maternal complex

Basic information

Region (hg38): 6:73362657-73364171

Previous symbols: [ "C6orf221" ]

Links

ENSG00000203908 ∙ NCBI:154288 ∙ OMIM:611687 ∙ HGNC:33699 ∙ Uniprot:Q587J8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hydatidiform mole, recurrent, 2 (Strong), mode of inheritance: AR
• complete hydatidiform mole (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hydatidiform mole, recurrent, 2	AR	Obstetric; Oncologic	Women are likely to have pregnancies with hydatidiform moles, with a high risk of persistent trophoblastic disease, including requiring chemotherapeutic treatment, and awareness may allow reproductive planning and/or surveillance measures, which may allow early detection and treatment	Obstetric; Oncologic	11932746; 19246479; 21623199; 21885028

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KHDC3L gene.

• Inborn genetic diseases (12 variants)
• Hydatidiform mole, recurrent, 2 (1 variants)
• Hydatidiform mole (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KHDC3L gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			12		1	13
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	12	0	1

Highest pathogenic variant AF is 0.00000657

Variants in KHDC3L

This is a list of pathogenic ClinVar variants found in the KHDC3L region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-73362730-A-G		Hydatidiform mole, recurrent, 2	Uncertain significance (Mar 29, 2024)
6-73362732-G-T		Hydatidiform mole, recurrent, 2	Pathogenic (Sep 09, 2011)
6-73362739-C-A		Inborn genetic diseases	Uncertain significance (Dec 05, 2022)
6-73362784-A-G		Inborn genetic diseases	Uncertain significance (Feb 14, 2024)
6-73362802-G-A		Inborn genetic diseases	Uncertain significance (Aug 10, 2023)
6-73362859-G-A		Inborn genetic diseases	Uncertain significance (Nov 05, 2021)
6-73362866-G-T		Inborn genetic diseases	Uncertain significance (Dec 22, 2023)
6-73363145-A-G		Inborn genetic diseases	Uncertain significance (Mar 12, 2024)
6-73363151-G-C		Inborn genetic diseases	Uncertain significance (Aug 26, 2022)
6-73363171-C-A		Inborn genetic diseases	Uncertain significance (Jan 26, 2022)
6-73363201-G-C		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
6-73363201-G-T		Inborn genetic diseases	Uncertain significance (Nov 29, 2023)
6-73363220-ACAAT-A		Hydatidiform mole, recurrent, 2	Pathogenic (Sep 01, 2013)
6-73363244-GCTGA-G		Hydatidiform mole, recurrent, 2	Pathogenic (Sep 01, 2013)
6-73363259-C-T		Hydatidiform mole, recurrent, 2	Likely pathogenic (Oct 16, 2014)
6-73363570-C-G		Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
6-73363588-A-C		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
6-73363604-C-T		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
6-73363619-T-C		Inborn genetic diseases	Likely benign (Dec 06, 2021)
6-73363682-C-G		Inborn genetic diseases	Uncertain significance (Nov 07, 2023)
6-73363730-A-T		Inborn genetic diseases	Uncertain significance (Jan 22, 2024)
6-73363760-C-A		Inborn genetic diseases	Uncertain significance (Apr 26, 2023)
6-73363778-C-A		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)
6-73363789-C-T		Inborn genetic diseases	Uncertain significance (Jan 06, 2023)
6-73363802-G-A		Inborn genetic diseases	Uncertain significance (Apr 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KHDC3L	protein_coding	protein_coding	ENST00000370367	3	1495

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.123	0.788	125741	0	2	125743	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.196	139	146	0.954	0.0000114	1389
Missense in Polyphen		34	38.795	0.87639		391
Synonymous	1.06	51	61.6	0.827	0.00000473	456
Loss of Function	1.36	2	5.41	0.370	3.02e-7	51

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Hydatidiform mole, recurrent, 2 (HYDM2) [MIM:614293]: A disorder characterized by excessive trophoblast development that produces a growing mass of tissue inside the uterus at the beginning of a pregnancy. It leads to abnormal pregnancies with no embryo, and cystic degeneration of the chorionic villi. {ECO:0000269|PubMed:21885028}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0846

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.0922
• hipred: N
• hipred_score: 0.247
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Khdc3
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: biological_process
• Cellular component: protein-containing complex
• Molecular function: RNA binding;protein binding