EFCAB13

EF-hand calcium binding domain 13, the group of EF-hand domain containing

Basic information

Region (hg38): 17:47323290-47441312

Previous symbols: [ "C17orf57" ]

Links

ENSG00000178852 ∙ NCBI:124989 ∙ ∙ HGNC:26864 ∙ Uniprot:Q8IY85 ∙ 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 EFCAB13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFCAB13 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				3	7	10
missense			36	1	7	44
nonsense				1	3	4
start loss						0
frameshift				1	1	2
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region					1	1
non coding				1		1
Total	0	0	36	7	19

Variants in EFCAB13

This is a list of pathogenic ClinVar variants found in the EFCAB13 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-47335222-T-G		not specified	Uncertain significance (Jul 12, 2022)
17-47335263-C-T		EFCAB13-related disorder	Benign (Feb 20, 2019)
17-47335305-A-C		not specified	Uncertain significance (Mar 24, 2023)
17-47335320-C-T		not specified	Uncertain significance (Jul 14, 2021)
17-47344197-G-A		EFCAB13-related disorder	Benign (Feb 19, 2019)
17-47344264-C-T		not specified	Uncertain significance (Sep 01, 2021)
17-47345080-C-G		not specified	Uncertain significance (Apr 26, 2024)
17-47347814-A-G		not specified	Uncertain significance (Dec 19, 2023)
17-47347815-T-C		EFCAB13-related disorder	Likely benign (Mar 10, 2022)
17-47347844-G-A		not specified	Uncertain significance (May 20, 2024)
17-47347921-C-T		EFCAB13-related disorder	Benign (Feb 19, 2019)
17-47361412-A-G		not specified	Uncertain significance (Sep 13, 2023)
17-47361422-C-T		EFCAB13-related disorder	Benign (Feb 20, 2019)
17-47361431-A-G		not specified	Uncertain significance (Mar 13, 2023)
17-47361455-G-C		not specified	Uncertain significance (Jan 23, 2024)
17-47361479-C-T		EFCAB13-related disorder	Benign (Nov 25, 2019)
17-47370436-G-A		EFCAB13-related disorder	Benign (Sep 30, 2019)
17-47370437-G-A		not specified	Uncertain significance (Jun 11, 2021)
17-47370454-A-G		not specified	Uncertain significance (Jul 25, 2023)
17-47370466-A-G		EFCAB13-related disorder	Benign (Nov 15, 2019)
17-47374501-A-G		not specified	Uncertain significance (Jul 19, 2023)
17-47374528-G-A		EFCAB13-related disorder	Benign (Oct 17, 2019)
17-47374565-G-A		not specified	Uncertain significance (May 15, 2024)
17-47374567-T-A		not specified	Uncertain significance (Apr 05, 2023)
17-47374626-A-G		EFCAB13-related disorder	Likely benign (Jan 20, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFCAB13	protein_coding	protein_coding	ENST00000331493	22	118023

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.45e-32	0.0000103	30848	30813	64078	125739	0.505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	412	473	0.870	0.0000225	6497
Missense in Polyphen		88	94.504	0.93118		1542
Synonymous	1.67	135	162	0.833	0.00000792	1660
Loss of Function	-0.417	46	43.0	1.07	0.00000196	645

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	1.05	0.958
Ashkenazi Jewish	0.572	0.558
East Asian	0.424	0.424
Finnish	0.528	0.524
European (Non-Finnish)	0.564	0.557
Middle Eastern	0.424	0.424
South Asian	0.483	0.465
Other	0.544	0.528

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.3

Haploinsufficiency Scores

• pHI: 0.0422
• hipred: N
• hipred_score: 0.146
• ghis: 0.425

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: Gm11639