EFHD1

EF-hand domain family member D1, the group of EF-hand domain containing

Basic information

Region (hg38): 2:232606057-232682776

Links

ENSG00000115468 ∙ NCBI:80303 ∙ OMIM:611617 ∙ HGNC:29556 ∙ Uniprot:Q9BUP0 ∙ 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 EFHD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFHD1 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			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in EFHD1

This is a list of pathogenic ClinVar variants found in the EFHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-232633762-G-A		not specified	Uncertain significance (Dec 02, 2022)
2-232633823-C-A		not specified	Uncertain significance (Oct 12, 2021)
2-232633849-G-C		not specified	Uncertain significance (Jul 27, 2022)
2-232633933-G-A		not specified	Uncertain significance (Jun 29, 2023)
2-232633942-C-T		not specified	Uncertain significance (Sep 30, 2021)
2-232633949-C-T		Anophthalmia-microphthalmia syndrome	Likely benign (Jan 01, 2013)
2-232634003-A-C		not specified	Uncertain significance (Feb 13, 2024)
2-232634003-A-G		not specified	Uncertain significance (May 09, 2022)
2-232662830-G-A		not specified	Uncertain significance (Feb 22, 2023)
2-232662869-G-A		not specified	Uncertain significance (May 26, 2024)
2-232662887-G-A		not specified	Uncertain significance (Dec 04, 2023)
2-232662902-A-G		not specified	Uncertain significance (Aug 21, 2023)
2-232681652-G-A		not specified	Likely benign (Nov 01, 2022)
2-232681657-G-A		not specified	Uncertain significance (Sep 25, 2023)
2-232681675-C-T		not specified	Uncertain significance (May 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFHD1	protein_coding	protein_coding	ENST00000264059	4	76725

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00515	0.719	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.128	119	123	0.968	0.00000683	1540
Missense in Polyphen		44	48.907	0.89966		604
Synonymous	0.627	47	52.8	0.890	0.00000288	471
Loss of Function	0.751	4	5.98	0.669	2.50e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000673	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000334	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a calcium sensor for mitochondrial flash (mitoflash) activation, an event characterized by stochastic bursts of superoxide production (PubMed:26975899). May play a role in neuronal differentiation (By similarity). {ECO:0000250|UniProtKB:Q9D4J1, ECO:0000269|PubMed:26975899}.

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.463
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.329
• hipred: N
• hipred_score: 0.498
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.931

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efhd1

Gene ontology

• Biological process: neuron projection development
• Cellular component: mitochondrial inner membrane
• Molecular function: calcium ion binding