EFCAB10

protein-coding

EF-hand calcium binding domain 10, the group of EF-hand domain containing

Gene summary

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

MANE transcript

NM_001355526.2

Inheritance

—

ClinVar variants

U:1B:2

Top phenotype

RINT1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr7:105,565,120-105,600,875

External References & Databases

Ensembl (ENSG00000185055)

NCBI Gene (100130771)

Transcript & Mutation Effects

hg38 • Region Span ~35.8 kb

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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 EFCAB10 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 222

not providedTotal: 121

RINT1-related disorderTotal: 6

Infantile liver failure syndrome 3Total: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001355526.2. 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						0
missense					1 clinvar	1
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar	1 clinvar		2
Total	0	0	1	1	1	3

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001355526.2	RefSeq	NP_001342455.1	5	MANE Select
ENST00000480514.6	Ensembl	ENSP00000418678.1	5	MANE Select
NM_001355527.2	RefSeq	NP_001342456.1	4	Standard
NM_001355529.2	RefSeq	NP_001342458.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

calcium ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000485614
Coding exons: 5
Length: 35756
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.439	60	70.4	0.853	0.00000332	977
Missense (PolyPhen)		16	19.786	0.80864		283
Synonymous	-0.210	28	26.6	1.05	0.00000141	262
Loss of Function	1.08	4	7.12	0.562	3.80e-7	108

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR2): S
Indispensability pred.: N
Indispensability score: 0.315

Gene Damage Prediction

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