EFCAB12

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

Basic information

Region (hg38): 3:129401321-129428636

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.

• not_specified (85 variants)
• Autism (1 variants)

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. These statistics are base on transcript: NM_000207307.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			78	8		86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	78	8	0

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