EFCAB12

protein-coding

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

Gene summary

Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C3orf25

MANE transcript

NM_207307.3

Inheritance

—

ClinVar variants

U:89B:10

Top phenotype

Autism

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr3:129,401,321-129,428,636

External References & Databases

Ensembl (ENSG00000172771)

Transcript & Mutation Effects

hg38 • Region Span ~27.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EFCAB12 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 91

AutismTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207307.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			84 clinvar	10 clinvar		94
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	89	10	0	99

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207307.3	RefSeq	NP_997190.1	9	MANE Select
ENST00000505956.6	Ensembl	ENSP00000420854.1	9	MANE Select
ENST00000503957.1	Ensembl	ENSP00000421462.1	4	Standard
ENST00001031038.1	Ensembl	ENSP00000700855.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

calcium ion binding
protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000505956
Coding exons: 9
Length: 27331
Individuals with no LoFs: 124468
Homozygous LoFs: 0
Heterozygous LoFs: 184
Defined: 124652
p: 0.000738

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.445	307	330	0.931	0.0000192	3733
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00032	0.00032	rare
Latino/Admixed American	0.00053	0.00052	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00017	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0012	0.0012	notable
South Asian	0.00056	0.00056	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 2.27
RVIS percentile EVS: 98.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N

Gene Damage Prediction

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