EFCAB10

EF-hand calcium binding domain 10, the group of EF-hand domain containing

Basic information

Region (hg38): 7:105565119-105600875

Links

ENSG00000185055 ∙ NCBI:100130771 ∙ ∙ HGNC:34531 ∙ Uniprot:A6NFE3 ∙ 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 EFCAB10 gene.

• Hereditary cancer-predisposing syndrome (202 variants)
• not provided (163 variants)
• Infantile liver failure syndrome 3 (4 variants)
• not specified (2 variants)
• Hereditary breast ovarian cancer syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFCAB10 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region			4	1		5
non coding	4	1	168	80	6	259
Total	4	1	168	81	6

Highest pathogenic variant AF is 0.00000657

Variants in EFCAB10

This is a list of pathogenic ClinVar variants found in the EFCAB10 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-105565262-A-G			Uncertain significance (Apr 12, 2021)
7-105565264-G-A			Likely benign (Jul 25, 2022)
7-105565265-T-G			Likely benign (Mar 22, 2022)
7-105565266-G-GT		not specified	Benign/Likely benign (Aug 29, 2023)
7-105565270-TTTCCAGATGG-T			Likely pathogenic (May 01, 2023)
7-105565271-T-C			Likely benign (Feb 11, 2022)
7-105565274-C-T		not specified	Uncertain significance (Mar 09, 2021)
7-105565277-A-T		not specified	Uncertain significance (Jul 05, 2022)
7-105565281-T-C		not specified	Likely benign (Jun 02, 2019)
7-105565281-T-G		not specified	Uncertain significance (Jul 26, 2022)
7-105565283-G-C		not specified	Uncertain significance (May 14, 2022)
7-105565285-C-G		not specified	Uncertain significance (Mar 08, 2024)
7-105565285-C-T		not specified	Uncertain significance (Feb 24, 2023)
7-105565287-T-C		not specified	Likely benign (Mar 27, 2023)
7-105565292-A-G		not specified	Likely benign (Oct 16, 2023)
7-105565296-C-T		not specified	Uncertain significance (Aug 05, 2020)
7-105565300-C-T		not specified	Uncertain significance (Jul 26, 2023)
7-105565305-C-T		not specified	Uncertain significance (Mar 11, 2022)
7-105565307-G-C		not specified	Uncertain significance (Oct 29, 2023)
7-105565309-CAGT-C		not specified	Uncertain significance (Jun 22, 2022)
7-105565310-A-T		not specified	Likely benign (Jul 22, 2021)
7-105565311-G-A		not specified	Uncertain significance (Mar 09, 2024)
7-105565313-G-A		not specified	Likely benign (Sep 24, 2021)
7-105565314-A-T			Uncertain significance (Jul 27, 2016)
7-105565315-T-C		not specified	Uncertain significance (Aug 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFCAB10	protein_coding	protein_coding	ENST00000485614	5	35756

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00899	0.820	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.439	60	70.4	0.853	0.00000332	977
Missense in Polyphen		16	19.786	0.80864		283
Synonymous	-0.210	28	26.6	1.05	0.00000141	262
Loss of Function	1.08	4	7.12	0.562	3.80e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.315

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efcab10

Gene ontology

• Molecular function: calcium ion binding