EFCAB14

EF-hand calcium binding domain 14, the group of EF-hand domain containing

Basic information

Region (hg38): 1:46674659-46719146

Previous symbols: [ "KIAA0494" ]

Links

ENSG00000159658 ∙ NCBI:9813 ∙ OMIM:619559 ∙ HGNC:29051 ∙ Uniprot:O75071 ∙ 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 EFCAB14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFCAB14 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in EFCAB14

This is a list of pathogenic ClinVar variants found in the EFCAB14 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-46678582-T-A		not specified	Uncertain significance (Sep 20, 2023)
1-46683332-G-C		not specified	Uncertain significance (Nov 09, 2023)
1-46683384-T-C		not specified	Uncertain significance (Jan 23, 2024)
1-46684500-C-T		not specified	Uncertain significance (Jun 22, 2024)
1-46684505-T-C		not specified	Uncertain significance (Sep 13, 2023)
1-46684545-T-C		not specified	Uncertain significance (Jun 02, 2023)
1-46684559-T-C		not specified	Uncertain significance (Apr 13, 2023)
1-46684601-T-C		not specified	Uncertain significance (Mar 07, 2024)
1-46688455-C-G		not specified	Uncertain significance (Mar 20, 2024)
1-46688472-G-A		not specified	Uncertain significance (Mar 20, 2024)
1-46689619-C-G		not specified	Uncertain significance (Jun 10, 2024)
1-46691829-T-C		not specified	Uncertain significance (Oct 25, 2023)
1-46691867-T-A		not specified	Uncertain significance (Jan 26, 2022)
1-46691898-G-T		not specified	Uncertain significance (Dec 12, 2023)
1-46696561-C-T		not specified	Uncertain significance (Mar 31, 2024)
1-46707932-T-C		not specified	Uncertain significance (Feb 22, 2023)
1-46707938-C-G		not specified	Uncertain significance (Feb 16, 2023)
1-46716369-G-A		not specified	Uncertain significance (Apr 14, 2022)
1-46716435-T-C		not specified	Uncertain significance (Dec 18, 2023)
1-46717920-A-C		not specified	Uncertain significance (Jan 29, 2024)
1-46717927-A-G		not specified	Uncertain significance (Dec 14, 2023)
1-46717978-G-A		not specified	Uncertain significance (Jun 30, 2023)
1-46717988-T-G		not specified	Uncertain significance (Mar 18, 2024)
1-46717990-C-A		not specified	Uncertain significance (Apr 05, 2023)
1-46718020-T-C		not specified	Uncertain significance (May 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFCAB14	protein_coding	protein_coding	ENST00000371933	11	60459

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.78e-8	0.906	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.394	247	265	0.932	0.0000137	3266
Missense in Polyphen		74	84.6	0.87471		1121
Synonymous	-0.514	108	101	1.06	0.00000557	948
Loss of Function	1.73	15	24.2	0.620	0.00000112	313

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000301	0.000301
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000163	0.000109
South Asian	0.00	0.00
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.71

Haploinsufficiency Scores

• pHI: 0.340
• hipred: N
• hipred_score: 0.196
• ghis: 0.628

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efcab14

Gene ontology

• Molecular function: calcium ion binding