EFCAB3

EF-hand calcium binding domain 3, the group of EF-hand domain containing

Basic information

Region (hg38): 17:62343941-62416480

Links

ENSG00000172421 ∙ NCBI:146779 ∙ OMIM:619567 ∙ HGNC:26379 ∙ Uniprot:Q8N7B9 ∙ 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 EFCAB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFCAB3 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			16		1	17
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	16	2	2

Variants in EFCAB3

This is a list of pathogenic ClinVar variants found in the EFCAB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-62370328-G-T			Benign (May 21, 2018)
17-62373824-G-C			Benign (Dec 31, 2019)
17-62387341-G-A		not specified	Uncertain significance (Oct 18, 2021)
17-62387399-G-C		not specified	Uncertain significance (Jun 02, 2024)
17-62391831-A-G		not specified	Uncertain significance (Dec 15, 2023)
17-62391835-C-T			Likely benign (Apr 06, 2018)
17-62391899-G-A		not specified	Uncertain significance (Mar 20, 2023)
17-62391923-A-C		not specified	Uncertain significance (Apr 17, 2023)
17-62391927-A-G		not specified	Uncertain significance (Oct 29, 2021)
17-62391930-A-G		not specified	Uncertain significance (Feb 27, 2024)
17-62391965-C-T			Benign/Likely benign (Mar 01, 2023)
17-62393578-G-A		not specified	Uncertain significance (Oct 19, 2021)
17-62395149-C-T		not specified	Uncertain significance (Oct 04, 2022)
17-62395190-T-C			Benign (Dec 31, 2019)
17-62406491-G-A		not specified	Uncertain significance (Dec 03, 2021)
17-62406536-C-T		not specified	Uncertain significance (Sep 17, 2021)
17-62407143-G-A		not specified	Uncertain significance (Dec 14, 2023)
17-62407159-C-A		not specified	Uncertain significance (Jul 13, 2021)
17-62407159-C-G		not specified	Uncertain significance (Jul 27, 2021)
17-62413831-G-A		not specified	Uncertain significance (Dec 18, 2023)
17-62416012-G-A		not specified	Uncertain significance (Feb 28, 2023)
17-62416018-G-A		not specified	Uncertain significance (Aug 14, 2023)
17-62416121-C-T			Benign (May 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFCAB3	protein_coding	protein_coding	ENST00000450662	12	46259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.48e-9	0.773	123449	29	2268	125746	0.00918

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.759	211	244	0.863	0.0000111	3250
Missense in Polyphen		68	72.784	0.93427		1058
Synonymous	-0.621	92	84.7	1.09	0.00000383	863
Loss of Function	1.50	17	25.1	0.677	0.00000140	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0217	0.0215
Ashkenazi Jewish	0.00181	0.00179
East Asian	0.000660	0.000653
Finnish	0.0458	0.0455
European (Non-Finnish)	0.00746	0.00738
Middle Eastern	0.000660	0.000653
South Asian	0.00138	0.00134
Other	0.00584	0.00572

dbNSFP

Source: dbNSFP

• Pathway: Pathways in clear cell renal cell carcinoma (Consensus)

Intolerance Scores

• loftool: 0.760
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.55

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.194

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: Efcab3
• Phenotype: normal phenotype

Gene ontology

• Molecular function: calcium ion binding