EFHC2
Basic information
Region (hg38): X:44147872-44343672
Previous symbols: [ "MRX74" ]
Links
Phenotypes
GenCC
Source:
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 EFHC2 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 | 4 | |||||
missense | 34 | 37 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 34 | 6 | 1 |
Variants in EFHC2
This is a list of pathogenic ClinVar variants found in the EFHC2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
X-44148804-C-G | not specified | Uncertain significance (Jul 19, 2023) | ||
X-44148819-G-T | not specified | Uncertain significance (May 05, 2023) | ||
X-44148885-A-G | Likely benign (Feb 01, 2023) | |||
X-44163941-G-A | not specified | Uncertain significance (Jan 29, 2024) | ||
X-44163981-C-A | not specified | Uncertain significance (Oct 02, 2023) | ||
X-44164007-T-C | not specified | Uncertain significance (Feb 06, 2023) | ||
X-44178470-C-T | not specified | Uncertain significance (Mar 26, 2024) | ||
X-44178493-C-T | not specified | Uncertain significance (Jan 04, 2024) | ||
X-44178494-G-A | not specified | Uncertain significance (Sep 22, 2023) | ||
X-44232527-T-A | Uncertain significance (Feb 07, 2024) | |||
X-44232527-T-C | not specified | Uncertain significance (Apr 22, 2022) | ||
X-44232536-C-T | not specified | Uncertain significance (Nov 30, 2021) | ||
X-44232562-C-T | Likely benign (May 01, 2022) | |||
X-44232582-C-G | not specified | Benign (Jun 20, 2014) | ||
X-44232585-C-T | Likely benign (Mar 03, 2015) | |||
X-44235318-T-C | not specified | Uncertain significance (May 30, 2023) | ||
X-44235320-T-C | Likely benign (Dec 01, 2022) | |||
X-44235338-T-A | not specified | Uncertain significance (Jun 07, 2024) | ||
X-44242166-G-A | not specified | Uncertain significance (Feb 23, 2023) | ||
X-44242169-T-C | not specified | Uncertain significance (Jan 30, 2024) | ||
X-44242187-C-T | not specified | Uncertain significance (Jun 17, 2024) | ||
X-44242253-G-A | not specified | Uncertain significance (Feb 05, 2024) | ||
X-44242263-G-A | not specified | Uncertain significance (Sep 30, 2021) | ||
X-44248278-C-T | not specified | Uncertain significance (Dec 08, 2023) | ||
X-44248304-G-A | not specified | Uncertain significance (Mar 07, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
EFHC2 | protein_coding | protein_coding | ENST00000420999 | 15 | 195791 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.999 | 0.000897 | 118292 | 0 | 1 | 118293 | 0.00000423 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.622 | 216 | 243 | 0.888 | 0.0000186 | 4929 |
Missense in Polyphen | 33 | 59.515 | 0.55448 | 1229 | ||
Synonymous | 0.281 | 85 | 88.4 | 0.962 | 0.00000670 | 1325 |
Loss of Function | 4.18 | 0 | 20.3 | 0.00 | 0.00000141 | 482 |
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) | 0.0000256 | 0.00000929 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
Recessive Scores
- pRec
- 0.0954
Intolerance Scores
- loftool
- rvis_EVS
- 0.6
- rvis_percentile_EVS
- 82.78
Haploinsufficiency Scores
- pHI
- 0.107
- hipred
- N
- hipred_score
- 0.473
- ghis
- 0.382
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.141
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Efhc2
- Phenotype
Gene ontology
- Biological process
- cellular response to leukemia inhibitory factor
- Cellular component
- Molecular function
- calcium ion binding;protein binding