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.

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.

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				1		1
missense			99	9		108
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	99	10	0

Variants in EFCAB6

This is a list of pathogenic ClinVar variants found in the EFCAB6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-43528872-A-C		not specified	Uncertain significance (Mar 19, 2024)
22-43528919-C-G		not specified	Uncertain significance (May 29, 2024)
22-43530828-G-A		not specified	Uncertain significance (Feb 06, 2023)
22-43530919-G-A		not specified	Uncertain significance (May 24, 2023)
22-43530927-G-C		not specified	Uncertain significance (Jun 19, 2024)
22-43530946-T-A		not specified	Uncertain significance (May 30, 2024)
22-43530955-C-T		not specified	Uncertain significance (May 18, 2022)
22-43534719-T-C		not specified	Uncertain significance (Nov 09, 2022)
22-43534779-T-C		not specified	Uncertain significance (Dec 28, 2023)
22-43534842-C-T		not specified	Uncertain significance (Jul 30, 2023)
22-43537388-G-A		not specified	Uncertain significance (Jun 11, 2021)
22-43537393-G-A		not specified	Likely benign (Apr 04, 2024)
22-43537437-T-C		not specified	Uncertain significance (Oct 16, 2023)
22-43537472-C-T		not specified	Uncertain significance (Oct 05, 2023)
22-43537477-C-A			Likely benign (Apr 01, 2023)
22-43537511-G-A		not specified	Uncertain significance (Feb 05, 2024)
22-43537527-C-T		not specified	Uncertain significance (Mar 25, 2022)
22-43540131-G-T		not specified	Uncertain significance (Feb 21, 2024)
22-43540143-G-A		not specified	Uncertain significance (Jan 02, 2024)
22-43540207-C-T		not specified	Likely benign (Nov 15, 2021)
22-43540225-C-A		not specified	Uncertain significance (Dec 12, 2023)
22-43540326-T-C		not specified	Uncertain significance (Mar 17, 2023)
22-43540349-T-G		not specified	Uncertain significance (Jun 11, 2021)
22-43540354-C-T		not specified	Uncertain significance (Feb 27, 2023)
22-43554892-C-T		not specified	Uncertain significance (Sep 30, 2021)

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

Gene ontology

• Cellular component: nucleoplasm
• Molecular function: calcium ion binding