EFCAB5

EF-hand calcium binding domain 5, the group of EF-hand domain containing

Basic information

Region (hg38): 17:29929200-30108452

Links

ENSG00000176927 ∙ NCBI:374786 ∙ ∙ HGNC:24801 ∙ Uniprot:A4FU69 ∙ 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 EFCAB5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFCAB5 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				8	3	11
missense			66	14	8	88
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region				2		2
non coding				1		1
Total	0	0	66	25	11

Variants in EFCAB5

This is a list of pathogenic ClinVar variants found in the EFCAB5 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-29929966-G-T		not specified	Uncertain significance (Jan 24, 2024)
17-29941809-G-C		not specified	Uncertain significance (Jan 09, 2024)
17-29941839-G-A			Likely benign (Feb 01, 2023)
17-29943586-G-A		not specified	Uncertain significance (Apr 26, 2024)
17-29943589-C-T		not specified	Likely benign (Feb 10, 2022)
17-29968791-A-G		EFCAB5-related disorder	Likely benign (Jun 18, 2021)
17-29968848-C-G		not specified	Uncertain significance (Dec 21, 2022)
17-29968909-A-T		not specified	Uncertain significance (Dec 16, 2022)
17-29968929-C-A		not specified	Uncertain significance (Apr 07, 2022)
17-29968952-C-T		not specified	Uncertain significance (Dec 18, 2023)
17-29969054-C-A		not specified	Uncertain significance (Feb 13, 2024)
17-29969064-A-G		not specified	Uncertain significance (Dec 12, 2023)
17-29969075-G-C		not specified	Uncertain significance (May 31, 2023)
17-29969088-C-T		not specified	Uncertain significance (Jan 04, 2024)
17-29969104-G-C			Likely benign (Mar 01, 2023)
17-29969150-C-A		EFCAB5-related disorder	Benign (Jun 06, 2019)
17-29969151-C-A		EFCAB5-related disorder	Benign (Jun 06, 2019)
17-29969207-G-A		not specified	Uncertain significance (Nov 30, 2021)
17-29969261-A-C		not specified	Uncertain significance (May 04, 2022)
17-29969284-C-A		not specified	Uncertain significance (May 14, 2024)
17-29969307-G-A		not specified	Uncertain significance (Mar 15, 2024)
17-29969313-T-C		not specified	Uncertain significance (Apr 01, 2024)
17-29969327-G-A		not specified	Uncertain significance (Jan 23, 2023)
17-29993218-T-C		not specified	Uncertain significance (Dec 20, 2023)
17-29993251-G-A		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFCAB5	protein_coding	protein_coding	ENST00000394835	23	179253

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.20e-23	0.945	122492	15	2132	124639	0.00865

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.890	672	740	0.908	0.0000360	9888
Missense in Polyphen		213	237.46	0.89699		3250
Synonymous	0.482	255	265	0.962	0.0000133	2693
Loss of Function	2.66	47	71.2	0.660	0.00000348	952

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0146	0.0145
Ashkenazi Jewish	0.00577	0.00548
East Asian	0.0197	0.0198
Finnish	0.0204	0.0197
European (Non-Finnish)	0.00915	0.00846
Middle Eastern	0.0197	0.0198
South Asian	0.00178	0.00173
Other	0.00722	0.00696

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.997
• rvis_EVS: 2.23
• rvis_percentile_EVS: 98.18

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.145

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0235

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efcab5

Gene ontology

• Molecular function: calcium ion binding