EFCC1

protein-coding

EF-hand and coiled-coil domain containing 1, 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:

C3orf73
CCDC48

MANE transcript

NM_001377500.1

Inheritance

—

ClinVar variants

U:112B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr3:129,001,304-129,040,742

External References & Databases

Ensembl (ENSG00000114654)

Transcript & Mutation Effects

hg38 • Region Span ~39.4 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 EFCC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 113

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001377500.1. 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			1 clinvar	2 clinvar		3
missense			109 clinvar	4 clinvar		113
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	112	6	0	118

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001377500.1	RefSeq	NP_001364429.1	8	MANE Select
ENST00000683648.1	Ensembl	ENSP00000507795.1	8	MANE Select
NM_001377501.1	RefSeq	NP_001364430.1	4	Standard
NM_024768.3	RefSeq	NP_079044.2	8	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: ENST00000480450
Coding exons: 8
Length: 39114
Individuals with no LoFs: 125645
Homozygous LoFs: 0
Heterozygous LoFs: 102
Defined: 125747
p: 0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.723	239	273	0.877	0.0000147	3731
Missense (PolyPhen)		79	89.428	0.88339		1283
Synonymous	-0.189	133	130	1.02	0.00000779	1315
Loss of Function	0.995	13	17.5	0.743	7.77e-7	241

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00035	0.00033	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00071	0.00071	rare
South Asian	0.00017	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0947

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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