EAF1

ELL associated factor 1

Basic information

Region (hg38): 3:15427597-15450635

Links

ENSG00000144597 ∙ NCBI:85403 ∙ OMIM:608315 ∙ HGNC:20907 ∙ Uniprot:Q96JC9 ∙ 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 EAF1 gene.

• Inborn genetic diseases (12 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EAF1 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	2

Variants in EAF1

This is a list of pathogenic ClinVar variants found in the EAF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-15427796-A-G		not specified	Uncertain significance (Sep 25, 2023)
3-15427820-A-G		not specified	Uncertain significance (Jun 28, 2023)
3-15429988-T-C		not specified	Uncertain significance (Feb 17, 2023)
3-15432190-A-T		not specified	Uncertain significance (Dec 14, 2023)
3-15432209-G-C		not specified	Uncertain significance (Dec 16, 2021)
3-15434369-C-G		not specified	Uncertain significance (Dec 08, 2023)
3-15434394-A-G		not specified	Uncertain significance (Mar 22, 2023)
3-15434411-G-A			Benign (Dec 31, 2019)
3-15434451-G-T		not specified	Uncertain significance (Feb 16, 2023)
3-15436375-T-C		not specified	Uncertain significance (Aug 02, 2023)
3-15436377-A-G		not specified	Uncertain significance (Aug 02, 2023)
3-15436408-C-T		not specified	Uncertain significance (Aug 16, 2022)
3-15436426-G-T		not specified	Uncertain significance (Sep 22, 2022)
3-15436433-C-T			Benign (Dec 31, 2019)
3-15436455-G-A		not specified	Uncertain significance (Aug 04, 2022)
3-15436462-A-G		not specified	Uncertain significance (Oct 12, 2022)
3-15436488-T-C		not specified	Uncertain significance (Nov 10, 2022)
3-15436540-G-A			Likely benign (Feb 01, 2023)
3-15450154-T-G		Congenital myasthenic syndrome 5	Uncertain significance (Jan 13, 2018)
3-15450236-G-A		Congenital myasthenic syndrome 5	Uncertain significance (Jan 13, 2018)
3-15450249-G-A		Congenital myasthenic syndrome 5	Benign (Jan 13, 2018)
3-15450352-A-C		Congenital myasthenic syndrome 5	Uncertain significance (Jan 12, 2018)
3-15450364-G-A		Congenital myasthenic syndrome 5	Uncertain significance (Jan 13, 2018)
3-15450367-G-A		Congenital myasthenic syndrome 5	Uncertain significance (Jan 13, 2018)
3-15450396-G-A		Congenital myasthenic syndrome 5	Uncertain significance (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EAF1	protein_coding	protein_coding	ENST00000396842	6	15259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0615	0.924	125728	0	18	125746	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	114	149	0.766	0.00000740	1767
Missense in Polyphen		22	32.632	0.67418		458
Synonymous	-0.0427	54	53.6	1.01	0.00000275	506
Loss of Function	2.13	4	11.9	0.335	5.90e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional transactivator of ELL and ELL2 elongation activities. {ECO:0000269|PubMed:11418481, ECO:0000269|PubMed:16006523}.
• Pathway: Gene expression (Transcription);RNA Polymerase II Pre-transcription Events;Formation of RNA Pol II elongation complex ;RNA Polymerase II Transcription;RNA Polymerase II Transcription Elongation (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.242
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.14

Haploinsufficiency Scores

• pHI: 0.147
• hipred: Y
• hipred_score: 0.651
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.830

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eaf1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: eaf1
• Affected structure: neuroectoderm
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: regulation of transcription, DNA-templated;transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter
• Cellular component: nucleoplasm;transcription elongation factor complex;Cajal body;nuclear body;nuclear speck;ELL-EAF complex;intracellular membrane-bounded organelle;intercellular bridge
• Molecular function: protein binding