EFHC2

EF-hand domain containing 2, the group of EF-hand domain containing

Basic information

Region (hg38): X:44147871-44343672

Previous symbols: [ "MRX74" ]

Links

ENSG00000183690 ∙ NCBI:80258 ∙ OMIM:300817 ∙ HGNC:26233 ∙ Uniprot:Q5JST6 ∙ 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 EFHC2 gene.

• Inborn genetic diseases (22 variants)
• not provided (9 variants)
• Ornithine carbamoyltransferase deficiency (1 variants)
• not specified (1 variants)
• X-linked intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFHC2 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				4		4
missense			23	2	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	6	1

Variants in EFHC2

This is a list of pathogenic ClinVar variants found in the EFHC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-44148804-C-G		not specified	Uncertain significance (Jul 19, 2023)
X-44148819-G-T		not specified	Uncertain significance (May 05, 2023)
X-44148885-A-G			Likely benign (Feb 01, 2023)
X-44163941-G-A		not specified	Uncertain significance (Jan 29, 2024)
X-44163981-C-A		not specified	Uncertain significance (Oct 02, 2023)
X-44164007-T-C		not specified	Uncertain significance (Feb 06, 2023)
X-44178493-C-T		not specified	Uncertain significance (Jan 04, 2024)
X-44178494-G-A		not specified	Uncertain significance (Sep 22, 2023)
X-44232527-T-A			Uncertain significance (Feb 07, 2024)
X-44232527-T-C		not specified	Uncertain significance (Apr 22, 2022)
X-44232536-C-T		not specified	Uncertain significance (Nov 30, 2021)
X-44232562-C-T			Likely benign (May 01, 2022)
X-44232582-C-G		not specified	Benign (Jun 20, 2014)
X-44232585-C-T			Likely benign (Mar 03, 2015)
X-44235318-T-C		not specified	Uncertain significance (May 30, 2023)
X-44235320-T-C			Likely benign (Dec 01, 2022)
X-44242166-G-A		not specified	Uncertain significance (Feb 23, 2023)
X-44242169-T-C		not specified	Uncertain significance (Jan 30, 2024)
X-44242253-G-A		not specified	Uncertain significance (Feb 05, 2024)
X-44242263-G-A		not specified	Uncertain significance (Sep 30, 2021)
X-44248278-C-T		not specified	Uncertain significance (Dec 08, 2023)
X-44248304-G-A		not specified	Uncertain significance (Mar 07, 2024)
X-44248815-G-A			Likely benign (Jan 01, 2023)
X-44248826-C-T		not specified	Uncertain significance (Jul 05, 2023)
X-44250240-C-T		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFHC2	protein_coding	protein_coding	ENST00000420999	15	195791

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000897	118292	0	1	118293	0.00000423

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.622	216	243	0.888	0.0000186	4929
Missense in Polyphen		33	59.515	0.55448		1229
Synonymous	0.281	85	88.4	0.962	0.00000670	1325
Loss of Function	4.18	0	20.3	0.00	0.00000141	482

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000256	0.00000929
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0954

Intolerance Scores

• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.78

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.473
• ghis: 0.382

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.141

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efhc2

Gene ontology

• Biological process: cellular response to leukemia inhibitory factor
• Molecular function: calcium ion binding;protein binding