EFCAB7

EF-hand calcium binding domain 7, the group of EF-hand domain containing

Basic information

Region (hg38): 1:63523372-63572693

Links

ENSG00000203965 ∙ NCBI:84455 ∙ OMIM:617632 ∙ HGNC:29379 ∙ Uniprot:A8K855 ∙ 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 EFCAB7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFCAB7 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			20	1	2	23
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	2

Variants in EFCAB7

This is a list of pathogenic ClinVar variants found in the EFCAB7 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-63525594-G-A		not specified	Uncertain significance (Jul 15, 2021)
1-63525597-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-63525624-C-T		not specified	Uncertain significance (Jun 02, 2023)
1-63525625-C-G		not specified	Uncertain significance (Nov 10, 2024)
1-63525747-C-A		not specified	Uncertain significance (Jun 03, 2022)
1-63531841-A-G		not specified	Uncertain significance (Nov 21, 2022)
1-63532716-T-G		not specified	Uncertain significance (Jun 29, 2023)
1-63532754-A-G		not specified	Uncertain significance (Feb 15, 2023)
1-63533523-A-G			Benign (Feb 25, 2018)
1-63533556-A-G		not specified	Uncertain significance (Dec 03, 2024)
1-63533559-G-A		not specified	Uncertain significance (Aug 12, 2024)
1-63534124-A-G		not specified	Uncertain significance (Jan 19, 2024)
1-63534182-G-A		not specified	Likely benign (Mar 05, 2024)
1-63534205-A-G		not specified	Uncertain significance (Dec 07, 2024)
1-63545930-G-T		not specified	Uncertain significance (Apr 01, 2024)
1-63545939-AG-A		Postaxial polydactyly	Uncertain significance (-)
1-63545947-T-G		not specified	Uncertain significance (Dec 28, 2022)
1-63546037-T-C		not specified	Uncertain significance (Oct 16, 2024)
1-63551817-G-A		not specified	Uncertain significance (Nov 29, 2023)
1-63557137-A-C		not specified	Uncertain significance (Mar 22, 2023)
1-63557139-G-A		not specified	Uncertain significance (Jun 10, 2024)
1-63561706-CAG-C		Postaxial polydactyly	Uncertain significance (-)
1-63561723-A-G		not specified	Uncertain significance (Nov 09, 2023)
1-63561775-C-T		not specified	Uncertain significance (Apr 11, 2023)
1-63561783-C-G		not specified	Uncertain significance (May 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFCAB7	protein_coding	protein_coding	ENST00000371088	13	49322

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.61e-17	0.0310	125568	0	172	125740	0.000684

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	255	306	0.834	0.0000142	4155
Missense in Polyphen		42	59.005	0.71181		856
Synonymous	1.04	93	107	0.872	0.00000531	1117
Loss of Function	0.687	28	32.2	0.869	0.00000183	420

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00187	0.00178
Ashkenazi Jewish	0.00	0.00
East Asian	0.00104	0.000816
Finnish	0.000468	0.000370
European (Non-Finnish)	0.000972	0.000835
Middle Eastern	0.00104	0.000816
South Asian	0.000620	0.000490
Other	0.000832	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the EvC complex that positively regulates ciliary Hedgehog (Hh) signaling. Required for the localization of the EVC2:EVC subcomplex at the base of primary cilia. {ECO:0000250|UniProtKB:Q8VDY4}.
• Pathway: Signal Transduction;Activation of SMO;Hedgehog ,on, state;Signaling by Hedgehog (Consensus)

Intolerance Scores

• loftool: 0.951
• rvis_EVS: 1.62
• rvis_percentile_EVS: 96.03

Haploinsufficiency Scores

• pHI: 0.0374
• hipred: N
• hipred_score: 0.146
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.151

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efcab7

Gene ontology

• Biological process: positive regulation of protein import into nucleus;positive regulation of transcription by RNA polymerase II;positive regulation of protein localization to ciliary membrane
• Cellular component: cilium;extrinsic component of membrane;ciliary membrane;plasma membrane protein complex
• Molecular function: calcium ion binding