EFCC1

EF-hand and coiled-coil domain containing 1, the group of EF-hand domain containing

Basic information

Region (hg38): 3:129001304-129040742

Previous symbols: [ "C3orf73", "CCDC48" ]

Links

ENSG00000114654 ∙ NCBI:79825 ∙ ∙ HGNC:25692 ∙ Uniprot:Q9HA90 ∙ 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 EFCC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFCC1 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				2		2
missense			44	2		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	4	0

Variants in EFCC1

This is a list of pathogenic ClinVar variants found in the EFCC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-129001632-G-A		not specified	Uncertain significance (Mar 02, 2023)
3-129001651-C-T		not specified	Uncertain significance (Mar 28, 2024)
3-129001669-G-T		not specified	Uncertain significance (May 17, 2023)
3-129001671-G-T		not specified	Uncertain significance (Aug 17, 2021)
3-129001680-G-C		not specified	Uncertain significance (Jul 11, 2023)
3-129001717-T-G		not specified	Uncertain significance (Nov 03, 2022)
3-129001726-C-T		not specified	Uncertain significance (Feb 03, 2022)
3-129001867-G-A		not specified	Uncertain significance (Sep 22, 2023)
3-129001896-G-A		not specified	Uncertain significance (Mar 29, 2023)
3-129001946-A-T		not specified	Uncertain significance (Jan 08, 2024)
3-129001984-C-T		not specified	Uncertain significance (May 20, 2024)
3-129002028-C-T		not specified	Uncertain significance (Jan 26, 2022)
3-129002029-G-C		not specified	Uncertain significance (Aug 22, 2023)
3-129002031-G-A		not specified	Uncertain significance (Jan 04, 2022)
3-129002139-G-A		not specified	Uncertain significance (Apr 12, 2022)
3-129002182-C-A		not specified	Uncertain significance (May 03, 2023)
3-129002212-C-G		not specified	Uncertain significance (Mar 30, 2024)
3-129002226-G-T		not specified	Uncertain significance (Jun 16, 2023)
3-129002253-A-C		not specified	Uncertain significance (May 23, 2023)
3-129003894-C-T		not specified	Uncertain significance (May 17, 2023)
3-129003908-G-T		not specified	Uncertain significance (Oct 24, 2023)
3-129003987-A-G		not specified	Uncertain significance (Jan 04, 2024)
3-129003993-T-A		not specified	Uncertain significance (Jun 24, 2022)
3-129004005-A-C		not specified	Uncertain significance (Nov 21, 2022)
3-129004005-A-G		not specified	Uncertain significance (Jan 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFCC1	protein_coding	protein_coding	ENST00000480450	8	39114

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.05e-7	0.551	125645	0	102	125747	0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.723	239	273	0.877	0.0000147	3731
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000348	0.000326
Finnish	0.000234	0.000231
European (Non-Finnish)	0.000714	0.000712
Middle Eastern	0.000348	0.000326
South Asian	0.000166	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0947

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.153
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Efcc1

Gene ontology

• Molecular function: calcium ion binding