EFHB

EF-hand domain family member B, the group of EF-hand domain containing|Cilia and flagella associated

Basic information

Region (hg38): 3:19879472-19947025

Links

ENSG00000163576 ∙ NCBI:151651 ∙ ∙ HGNC:26330 ∙ Uniprot:Q8N7U6 ∙ 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 EFHB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFHB 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			40	3		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	4	0

Variants in EFHB

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

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

Position	Type	Phenotype	Significance	ClinVar
3-19879757-T-G		not specified	Uncertain significance (Oct 17, 2023)
3-19879803-A-G		not specified	Uncertain significance (Aug 22, 2023)
3-19882562-T-A		not specified	Uncertain significance (Feb 23, 2023)
3-19882592-T-G			Likely benign (Aug 25, 2017)
3-19882626-G-A		not specified	Uncertain significance (Jun 16, 2024)
3-19882633-C-A		not specified	Uncertain significance (Aug 02, 2021)
3-19882639-C-G		not specified	Uncertain significance (Mar 29, 2022)
3-19882672-G-A		not specified	Uncertain significance (Dec 20, 2021)
3-19882678-T-A		not specified	Uncertain significance (Apr 20, 2024)
3-19884496-G-A		not specified	Uncertain significance (May 16, 2024)
3-19884577-C-T		not specified	Uncertain significance (Mar 01, 2023)
3-19884600-C-G		not specified	Uncertain significance (Feb 02, 2024)
3-19884607-G-A		not specified	Uncertain significance (Dec 13, 2023)
3-19888453-T-C		not specified	Uncertain significance (Jun 22, 2023)
3-19888467-T-A		not specified	Uncertain significance (Oct 05, 2023)
3-19888510-C-T		not specified	Uncertain significance (Apr 20, 2024)
3-19888525-T-C		not specified	Uncertain significance (Jan 30, 2024)
3-19888554-T-C		not specified	Uncertain significance (May 05, 2023)
3-19888592-C-G		not specified	Uncertain significance (Feb 22, 2023)
3-19888615-C-G		not specified	Uncertain significance (May 29, 2024)
3-19896743-T-G			Likely benign (Aug 25, 2017)
3-19896757-C-T		not specified	Uncertain significance (May 02, 2024)
3-19896758-G-A		not specified	Uncertain significance (Dec 09, 2023)
3-19896760-A-G		not specified	Uncertain significance (Feb 02, 2022)
3-19896759-A-AAC			Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFHB	protein_coding	protein_coding	ENST00000295824	13	67554

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.80e-24	0.00137	124327	21	1245	125593	0.00505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.242	448	434	1.03	0.0000222	5426
Missense in Polyphen		66	60.114	1.0979		751
Synonymous	1.20	130	149	0.875	0.00000732	1581
Loss of Function	0.333	37	39.3	0.943	0.00000240	496

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0274	0.0274
Ashkenazi Jewish	0.000103	0.0000993
East Asian	0.00920	0.00901
Finnish	0.00	0.00
European (Non-Finnish)	0.00145	0.00145
Middle Eastern	0.00920	0.00901
South Asian	0.000729	0.000686
Other	0.00428	0.00425

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.983
• rvis_EVS: 1.96
• rvis_percentile_EVS: 97.55

Haploinsufficiency Scores

• pHI: 0.0727
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0834

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efhb

Gene ontology

• Molecular function: calcium ion binding