EFCAB12

EF-hand calcium binding domain 12, the group of EF-hand domain containing

Basic information

Region (hg38): 3:129401320-129428651

Previous symbols: [ "C3orf25" ]

Links

ENSG00000172771 ∙ NCBI:90288 ∙ ∙ HGNC:28061 ∙ Uniprot:Q6NXP0 ∙ 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 EFCAB12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFCAB12 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			25	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	25	1	0

Variants in EFCAB12

This is a list of pathogenic ClinVar variants found in the EFCAB12 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-129401624-T-C		not specified	Uncertain significance (Jun 07, 2023)
3-129401687-G-A		not specified	Uncertain significance (Jul 14, 2021)
3-129401739-G-A		not specified	Uncertain significance (May 16, 2024)
3-129401792-G-A		not specified	Uncertain significance (Nov 08, 2022)
3-129404298-A-T		not specified	Uncertain significance (Jun 19, 2024)
3-129404346-C-T		not specified	Uncertain significance (Aug 04, 2023)
3-129404388-C-T		not specified	Uncertain significance (Dec 15, 2022)
3-129408743-A-G		not specified	Uncertain significance (Aug 02, 2022)
3-129408812-C-T		not specified	Uncertain significance (Jan 09, 2024)
3-129408818-A-G		not specified	Uncertain significance (Jan 24, 2023)
3-129408825-A-G		not specified	Uncertain significance (Jun 04, 2024)
3-129408852-T-C		not specified	Uncertain significance (Mar 26, 2024)
3-129411187-G-A		not specified	Uncertain significance (Jun 13, 2024)
3-129411225-C-T		not specified	Uncertain significance (Mar 25, 2024)
3-129411258-G-A		not specified	Uncertain significance (May 16, 2024)
3-129411274-T-C		not specified	Uncertain significance (Jun 09, 2022)
3-129415298-T-C		not specified	Uncertain significance (Oct 16, 2023)
3-129415365-T-C		not specified	Likely benign (Jul 05, 2023)
3-129418267-G-A		not specified	Uncertain significance (Jul 20, 2021)
3-129418312-A-G		not specified	Uncertain significance (Dec 07, 2021)
3-129418345-C-A		not specified	Uncertain significance (Apr 22, 2024)
3-129418372-G-A		not specified	Uncertain significance (Dec 28, 2022)
3-129418434-C-A		not specified	Uncertain significance (Dec 06, 2022)
3-129418447-T-C		not specified	Uncertain significance (May 18, 2022)
3-129421455-G-A		not specified	Uncertain significance (May 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFCAB12	protein_coding	protein_coding	ENST00000505956	9	27331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000154	0.993	124468	0	184	124652	0.000738

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.445	307	330	0.931	0.0000192	3733
Missense in Polyphen		85	93.753	0.90663		1120
Synonymous	0.329	130	135	0.964	0.00000805	1086
Loss of Function	2.39	12	24.9	0.483	0.00000131	278

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000854	0.000853
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.00124	0.00123
Middle Eastern	0.000167	0.000167
South Asian	0.000559	0.000556
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 2.27
• rvis_percentile_EVS: 98.23

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.123
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efcab12

Gene ontology

• Molecular function: calcium ion binding;protein binding