EDF1

endothelial differentiation related factor 1, the group of Cilia and flagella associated

Basic information

Region (hg38): 9:136862118-136866308

Links

ENSG00000107223 ∙ NCBI:8721 ∙ OMIM:605107 ∙ HGNC:3164 ∙ Uniprot:O60869 ∙ 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 EDF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EDF1 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						0
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in EDF1

This is a list of pathogenic ClinVar variants found in the EDF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136862291-G-A		not specified	Uncertain significance (Mar 05, 2024)
9-136862328-T-C		not specified	Uncertain significance (Mar 17, 2023)
9-136862333-C-T		not specified	Uncertain significance (Sep 16, 2021)
9-136866216-T-G		not specified	Uncertain significance (Nov 10, 2022)
9-136866236-G-A		not specified	Uncertain significance (Aug 08, 2023)
9-136866247-G-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EDF1	protein_coding	protein_coding	ENST00000224073	5	4168

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.777	0.221	125670	0	2	125672	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	52	94.6	0.550	0.00000577	955
Missense in Polyphen		12	23.945	0.50115		232
Synonymous	-1.94	53	37.8	1.40	0.00000230	290
Loss of Function	2.53	1	9.32	0.107	4.96e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional coactivator stimulating NR5A1 and ligand-dependent NR1H3/LXRA and PPARG transcriptional activities. Enhances the DNA-binding activity of ATF1, ATF2, CREB1 and NR5A1. Regulates nitric oxid synthase activity probably by sequestering calmodulin in the cytoplasm. May function in endothelial cells differentiation, hormone-induced cardiomyocytes hypertrophy and lipid metabolism. {ECO:0000269|PubMed:10567391, ECO:0000269|PubMed:12040021, ECO:0000269|PubMed:15112053, ECO:0000269|PubMed:9813014}.

Recessive Scores

• pRec: 0.186

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.563
• hipred: Y
• hipred_score: 0.783
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Edf1

Gene ontology

• Biological process: regulation of transcription, DNA-templated;multicellular organism development;regulation of lipid metabolic process;positive regulation of DNA binding;endothelial cell differentiation;positive regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleolus;cytoplasm;cytosol
• Molecular function: TFIID-class transcription factor complex binding;transcription coactivator activity;RNA binding;protein binding;calmodulin binding;sequence-specific DNA binding