KHDC3L
Basic information
Region (hg38): 6:73362658-73364171
Previous symbols: [ "C6orf221" ]
Links
Phenotypes
GenCC
Source:
- hydatidiform mole, recurrent, 2 (Strong), mode of inheritance: AR
- complete hydatidiform mole (Supportive), mode of inheritance: AR
Clinical Genomic Database
Source:
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
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 | 21 | 23 | ||||
nonsense | 1 | |||||
start loss | 1 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 1 | 22 | 1 | 1 |
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 (Dec 10, 2024) | ||
6-73362866-G-T | Inborn genetic diseases | Uncertain significance (Dec 22, 2023) | ||
6-73363120-C-A | Inborn genetic diseases | Uncertain significance (Apr 01, 2024) | ||
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 • KHDC3L-related condition | Pathogenic (May 31, 2024) | ||
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) | ||
6-73363609-C-T | Inborn genetic diseases | Uncertain significance (Dec 04, 2024) | ||
6-73363610-G-C | Inborn genetic diseases | Uncertain significance (Aug 26, 2024) | ||
6-73363619-T-C | Inborn genetic diseases | Likely benign (Dec 06, 2021) | ||
6-73363640-C-A | Inborn genetic diseases | Uncertain significance (Aug 14, 2024) | ||
6-73363682-C-G | Inborn genetic diseases | Uncertain significance (Nov 07, 2023) | ||
6-73363730-A-T | Inborn genetic diseases | Uncertain significance (Jan 22, 2024) |
GnomAD
Source:
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:
- 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
- loftool
- 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_indispensability_pred
- gene_indispensability_score
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