EFCAB13
Basic information
Region (hg38): 17:47323290-47441312
Previous symbols: [ "C17orf57" ]
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 EFCAB13 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 | 10 | |||||
missense | 36 | 44 | ||||
nonsense | 4 | |||||
start loss | 0 | |||||
frameshift | 2 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 1 | 1 | ||||
non coding | 1 | |||||
Total | 0 | 0 | 36 | 7 | 19 |
Variants in EFCAB13
This is a list of pathogenic ClinVar variants found in the EFCAB13 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
17-47335222-T-G | not specified | Uncertain significance (Jul 12, 2022) | ||
17-47335263-C-T | EFCAB13-related disorder | Benign (Feb 20, 2019) | ||
17-47335305-A-C | not specified | Uncertain significance (Mar 24, 2023) | ||
17-47335320-C-T | not specified | Uncertain significance (Jul 14, 2021) | ||
17-47344197-G-A | EFCAB13-related disorder | Benign (Feb 19, 2019) | ||
17-47344264-C-T | not specified | Uncertain significance (Sep 01, 2021) | ||
17-47345080-C-G | not specified | Uncertain significance (Apr 26, 2024) | ||
17-47347814-A-G | not specified | Uncertain significance (Dec 19, 2023) | ||
17-47347815-T-C | EFCAB13-related disorder | Likely benign (Mar 10, 2022) | ||
17-47347844-G-A | not specified | Uncertain significance (May 20, 2024) | ||
17-47347921-C-T | EFCAB13-related disorder | Benign (Feb 19, 2019) | ||
17-47361412-A-G | not specified | Uncertain significance (Sep 13, 2023) | ||
17-47361422-C-T | EFCAB13-related disorder | Benign (Feb 20, 2019) | ||
17-47361431-A-G | not specified | Uncertain significance (Mar 13, 2023) | ||
17-47361455-G-C | not specified | Uncertain significance (Jan 23, 2024) | ||
17-47361479-C-T | EFCAB13-related disorder | Benign (Nov 25, 2019) | ||
17-47370436-G-A | EFCAB13-related disorder | Benign (Sep 30, 2019) | ||
17-47370437-G-A | not specified | Uncertain significance (Jun 11, 2021) | ||
17-47370454-A-G | not specified | Uncertain significance (Jul 25, 2023) | ||
17-47370466-A-G | EFCAB13-related disorder | Benign (Nov 15, 2019) | ||
17-47374501-A-G | not specified | Uncertain significance (Jul 19, 2023) | ||
17-47374528-G-A | EFCAB13-related disorder | Benign (Oct 17, 2019) | ||
17-47374565-G-A | not specified | Uncertain significance (May 15, 2024) | ||
17-47374567-T-A | not specified | Uncertain significance (Apr 05, 2023) | ||
17-47374626-A-G | EFCAB13-related disorder | Likely benign (Jan 20, 2020) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
EFCAB13 | protein_coding | protein_coding | ENST00000331493 | 22 | 118023 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
6.45e-32 | 0.0000103 | 30848 | 30813 | 64078 | 125739 | 0.505 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.00 | 412 | 473 | 0.870 | 0.0000225 | 6497 |
Missense in Polyphen | 88 | 94.504 | 0.93118 | 1542 | ||
Synonymous | 1.67 | 135 | 162 | 0.833 | 0.00000792 | 1660 |
Loss of Function | -0.417 | 46 | 43.0 | 1.07 | 0.00000196 | 645 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 1.05 | 0.958 |
Ashkenazi Jewish | 0.572 | 0.558 |
East Asian | 0.424 | 0.424 |
Finnish | 0.528 | 0.524 |
European (Non-Finnish) | 0.564 | 0.557 |
Middle Eastern | 0.424 | 0.424 |
South Asian | 0.483 | 0.465 |
Other | 0.544 | 0.528 |
dbNSFP
Source:
Intolerance Scores
- loftool
- rvis_EVS
- 0.89
- rvis_percentile_EVS
- 89.3
Haploinsufficiency Scores
- pHI
- 0.0422
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.425
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
- Gm11639
- Phenotype