EFCAB13

EF-hand calcium binding domain 13, the group of EF-hand domain containing

Basic information

Region (hg38): 17:47323290-47441312

Previous symbols: [ "C17orf57" ]

Links

ENSG00000178852NCBI:124989HGNC:26864Uniprot:Q8IY85AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EFCAB13 gene.

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
3
clinvar
7
clinvar
10
missense
36
clinvar
1
clinvar
7
clinvar
44
nonsense
1
clinvar
3
clinvar
4
start loss
0
frameshift
1
clinvar
1
clinvar
2
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
1
1
non coding
1
clinvar
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)2300890
17-47335263-C-T EFCAB13-related disorder Benign (Feb 20, 2019)3050458
17-47335305-A-C not specified Uncertain significance (Mar 24, 2023)2517727
17-47335320-C-T not specified Uncertain significance (Jul 14, 2021)2394076
17-47344197-G-A EFCAB13-related disorder Benign (Feb 19, 2019)3039578
17-47344264-C-T not specified Uncertain significance (Sep 01, 2021)2383369
17-47345080-C-G not specified Uncertain significance (Apr 26, 2024)2246150
17-47347814-A-G not specified Uncertain significance (Dec 19, 2023)3087410
17-47347815-T-C EFCAB13-related disorder Likely benign (Mar 10, 2022)3049648
17-47347844-G-A not specified Uncertain significance (May 20, 2024)3274603
17-47347921-C-T EFCAB13-related disorder Benign (Feb 19, 2019)3059359
17-47361412-A-G not specified Uncertain significance (Sep 13, 2023)2595403
17-47361422-C-T EFCAB13-related disorder Benign (Feb 20, 2019)3041441
17-47361431-A-G not specified Uncertain significance (Mar 13, 2023)2454605
17-47361455-G-C not specified Uncertain significance (Jan 23, 2024)3087411
17-47361479-C-T EFCAB13-related disorder Benign (Nov 25, 2019)3049039
17-47370436-G-A EFCAB13-related disorder Benign (Sep 30, 2019)3055475
17-47370437-G-A not specified Uncertain significance (Jun 11, 2021)2232581
17-47370454-A-G not specified Uncertain significance (Jul 25, 2023)2614461
17-47370466-A-G EFCAB13-related disorder Benign (Nov 15, 2019)3059163
17-47374501-A-G not specified Uncertain significance (Jul 19, 2023)2612624
17-47374528-G-A EFCAB13-related disorder Benign (Oct 17, 2019)3059444
17-47374565-G-A not specified Uncertain significance (May 15, 2024)3274607
17-47374567-T-A not specified Uncertain significance (Apr 05, 2023)2515506
17-47374626-A-G EFCAB13-related disorder Likely benign (Jan 20, 2020)3051249

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EFCAB13protein_codingprotein_codingENST00000331493 22118023
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
6.45e-320.00001033084830813640781257390.505
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.004124730.8700.00002256497
Missense in Polyphen8894.5040.931181542
Synonymous1.671351620.8330.000007921660
Loss of Function-0.4174643.01.070.00000196645

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American1.050.958
Ashkenazi Jewish0.5720.558
East Asian0.4240.424
Finnish0.5280.524
European (Non-Finnish)0.5640.557
Middle Eastern0.4240.424
South Asian0.4830.465
Other0.5440.528

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Gm11639
Phenotype