EFCAB6

EF-hand calcium binding domain 6, the group of EF-hand domain containing

Basic information

Region (hg38): 22:43528744-43812337

Links

ENSG00000186976

∙ NCBI:64800 ∙ OMIM:619664 ∙ HGNC:24204 ∙ Uniprot:Q5THR3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EFCAB6 gene.

not_specified (242 variants)
not_provided (5 variants)
Prostate_cancer (1 variants)
Abnormal_sperm_morphology (1 variants)
Reduced_sperm_motility (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFCAB6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022785.4. Only rare variants are included in the table.

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				2 clinvar		2
missense			227 clinvar	18 clinvar		245
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	227	20	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFCAB6	protein_coding	protein_coding	ENST00000262726	30	283594

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-45	0.00000110	123319	18	2411	125748	0.00971

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.257	843	822	1.03	0.0000454	9936
Missense in Polyphen		221	224.81	0.98304		2797
Synonymous	-0.591	340	326	1.04	0.0000209	2755
Loss of Function	0.399	71	74.7	0.950	0.00000375	939

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00676	0.00676
Ashkenazi Jewish	0.00646	0.00647
East Asian	0.0203	0.0203
Finnish	0.0148	0.0148
European (Non-Finnish)	0.00971	0.00958
Middle Eastern	0.0203	0.0203
South Asian	0.0112	0.0111
Other	0.00881	0.00883

dbNSFP

Source: dbNSFP

Function: FUNCTION: Negatively regulates the androgen receptor by recruiting histone deacetylase complex, and protein DJ-1 antagonizes this inhibition by abrogation of this complex. {ECO:0000269|PubMed:12612053}.;
Pathway: Androgen receptor signaling pathway;AndrogenReceptor (Consensus)

Recessive Scores

pRec: 0.0853

Intolerance Scores

loftool: 0.982
rvis_EVS: 2.23
rvis_percentile_EVS: 98.17

Haploinsufficiency Scores

pHI: 0.0848
hipred: N
hipred_score: 0.179
ghis: 0.412

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.333

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Efcab6
Phenotype

Gene ontology

Biological process
Cellular component: nucleoplasm
Molecular function: calcium ion binding