EFHD2

EF-hand domain family member D2, the group of EF-hand domain containing

Basic information

Region (hg38): 1:15409887-15430339

Links

ENSG00000142634 ∙ NCBI:79180 ∙ OMIM:616450 ∙ HGNC:28670 ∙ Uniprot:Q96C19 ∙ 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 EFHD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFHD2 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in EFHD2

This is a list of pathogenic ClinVar variants found in the EFHD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-15409984-G-A		not specified	Uncertain significance (Mar 07, 2023)
1-15410045-C-T		not specified	Uncertain significance (Aug 02, 2021)
1-15410081-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-15410087-G-A		not specified	Uncertain significance (Nov 17, 2022)
1-15410102-C-T		not specified	Uncertain significance (Feb 11, 2022)
1-15410104-G-A		not specified	Uncertain significance (May 09, 2024)
1-15425896-A-G		not specified	Uncertain significance (Jan 03, 2024)
1-15427219-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-15427220-G-A		not specified	Uncertain significance (Dec 14, 2021)
1-15427268-G-A		not specified	Uncertain significance (Jan 27, 2022)
1-15428598-G-C		not specified	Uncertain significance (May 15, 2023)
1-15428599-G-A		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFHD2	protein_coding	protein_coding	ENST00000375980	4	20449

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00910	0.822	125703	0	5	125708	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.963	96	126	0.759	0.00000734	1576
Missense in Polyphen		33	50.879	0.6486		579
Synonymous	-0.134	56	54.7	1.02	0.00000356	451
Loss of Function	1.09	4	7.15	0.560	3.02e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000351	0.0000351
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000109
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.00000899	0.00000879
Middle Eastern	0.000114	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate B-cell receptor (BCR)-induced immature and primary B-cell apoptosis. Plays a role as negative regulator of the canonical NF-kappa-B-activating branch. Controls spontaneous apoptosis through the regulation of BCL2L1 abundance. {ECO:0000250}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.414
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.255
• hipred: Y
• hipred_score: 0.516
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.194

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efhd2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype

Gene ontology

• Cellular component: membrane raft
• Molecular function: calcium ion binding;cadherin binding