EFCAB11

EF-hand calcium binding domain 11, the group of EF-hand domain containing

Basic information

Region (hg38): 14:89794668-89954777

Previous symbols: [ "C14orf143" ]

Links

ENSG00000140025 ∙ NCBI:90141 ∙ ∙ HGNC:20357 ∙ Uniprot:Q9BUY7 ∙ 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 EFCAB11 gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFCAB11 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						0
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in EFCAB11

This is a list of pathogenic ClinVar variants found in the EFCAB11 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-89797247-G-A		not specified	Uncertain significance (Jul 12, 2023)
14-89797305-C-G		not specified	Uncertain significance (Aug 13, 2021)
14-89931568-G-A		not specified	Uncertain significance (Jan 06, 2023)
14-89931628-C-T		not specified	Uncertain significance (Feb 14, 2023)
14-89931629-G-A		not specified	Uncertain significance (Jan 16, 2024)
14-89932560-T-G		not specified	Uncertain significance (Feb 16, 2023)
14-89932613-C-T		not specified	Uncertain significance (Aug 30, 2022)
14-89932616-C-T		not specified	Uncertain significance (Jan 18, 2023)
14-89953968-A-G		not specified	Uncertain significance (Aug 04, 2023)
14-89954593-C-G		not specified	Uncertain significance (Dec 28, 2022)
14-89954605-T-G		not specified	Uncertain significance (Dec 01, 2022)
14-89954656-A-G		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFCAB11	protein_coding	protein_coding	ENST00000316738	6	160109

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000232	0.768	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.440	99	87.4	1.13	0.00000450	1065
Missense in Polyphen		12	17.645	0.68008		249
Synonymous	0.750	25	30.2	0.827	0.00000156	281
Loss of Function	1.06	7	10.7	0.652	6.18e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000924	0.0000924
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000490	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.0000624	0.0000615
Middle Eastern	0.000490	0.000489
South Asian	0.000132	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: 0.7
• rvis_percentile_EVS: 85.42

Haploinsufficiency Scores

• pHI: 0.285
• hipred: N
• hipred_score: 0.231
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efcab11

Gene ontology

• Molecular function: calcium ion binding