EFHC2

EF-hand domain containing 2, the group of EF-hand domain containing

Basic information

Region (hg38): X:44147872-44343672

Previous symbols: [ "MRX74" ]

Links

ENSG00000183690NCBI:80258OMIM:300817HGNC:26233Uniprot:Q5JST6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EFHC2 gene.

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
clinvar
4
missense
34
clinvar
2
clinvar
1
clinvar
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)2588567
X-44148819-G-T not specified Uncertain significance (May 05, 2023)2544176
X-44148885-A-G Likely benign (Feb 01, 2023)2660362
X-44163941-G-A not specified Uncertain significance (Jan 29, 2024)3087553
X-44163981-C-A not specified Uncertain significance (Oct 02, 2023)3087552
X-44164007-T-C not specified Uncertain significance (Feb 06, 2023)2456442
X-44178470-C-T not specified Uncertain significance (Mar 26, 2024)3274687
X-44178493-C-T not specified Uncertain significance (Jan 04, 2024)3087551
X-44178494-G-A not specified Uncertain significance (Sep 22, 2023)3087550
X-44232527-T-A Uncertain significance (Feb 07, 2024)3235723
X-44232527-T-C not specified Uncertain significance (Apr 22, 2022)2360713
X-44232536-C-T not specified Uncertain significance (Nov 30, 2021)2262551
X-44232562-C-T Likely benign (May 01, 2022)2660363
X-44232582-C-G not specified Benign (Jun 20, 2014)193745
X-44232585-C-T Likely benign (Mar 03, 2015)1318353
X-44235318-T-C not specified Uncertain significance (May 30, 2023)2518660
X-44235320-T-C Likely benign (Dec 01, 2022)2660364
X-44235338-T-A not specified Uncertain significance (Jun 07, 2024)3274689
X-44242166-G-A not specified Uncertain significance (Feb 23, 2023)2488697
X-44242169-T-C not specified Uncertain significance (Jan 30, 2024)3087549
X-44242187-C-T not specified Uncertain significance (Jun 17, 2024)3274686
X-44242253-G-A not specified Uncertain significance (Feb 05, 2024)3087548
X-44242263-G-A not specified Uncertain significance (Sep 30, 2021)2209439
X-44248278-C-T not specified Uncertain significance (Dec 08, 2023)3087547
X-44248304-G-A not specified Uncertain significance (Mar 07, 2024)3087546

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EFHC2protein_codingprotein_codingENST00000420999 15195791
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9990.000897118292011182930.00000423
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6222162430.8880.00001864929
Missense in Polyphen3359.5150.554481229
Synonymous0.2818588.40.9620.000006701325
Loss of Function4.18020.30.000.00000141482

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00002560.00000929
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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