ELP1

elongator acetyltransferase complex subunit 1, the group of Elongator acetyltransferase complex

Basic information

Region (hg38): 9:108866898-108934328

Previous symbols: [ "DYS", "IKBKAP" ]

Links

ENSG00000070061 ∙ NCBI:8518 ∙ OMIM:603722 ∙ HGNC:5959 ∙ Uniprot:O95163 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary dysautonomia (Definitive), mode of inheritance: AR
• Riley-Day syndrome (Supportive), mode of inheritance: AR
• medulloblastoma (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neuropathy, hereditary sensory and autonomic, type III	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic; Renal	18118947; 14071043; 14245781; 4322121; 7374014; 7254974; 7097419; 3585611; 11179021; 11179008; 12406829; 12546638; 15088259; 19651702; 19914433; 20301359; 22129610; 22170819; 22229594; 22571291; 22727867; 22739220; 22850346
One report has described possible increased tumorigenesis in affected individuals; Individuals may be prone to injury due to pain insensitivity

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ELP1 gene.

• not provided (103 variants)
• not specified (6 variants)
• Familial dysautonomia (2 variants)
• Medulloblastoma (1 variants)
• Charcot-Marie-Tooth disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELP1 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	520	6	528
missense		2	508	12	7	529
nonsense	45	26	4			75
start loss		1	1			2
frameshift	61	46	2			109
inframe indel			15			15
splice donor/acceptor (+/-2bp)		72	2	2		76
splice region	1	2	37	105	1	146
non coding	1	1	54	313	111	480
Total	107	148	588	847	124

Highest pathogenic variant AF is 0.000506

Variants in ELP1

This is a list of pathogenic ClinVar variants found in the ELP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-108867549-T-C		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867604-A-G		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867621-T-C		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867626-C-T		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867686-G-A		Familial dysautonomia	Uncertain significance (Jan 12, 2018)
9-108867687-C-A		Familial dysautonomia	Uncertain significance (Jan 12, 2018)
9-108867703-A-T		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867709-T-C		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867763-T-C		Familial dysautonomia	Uncertain significance (Jan 12, 2018)
9-108867764-G-T		Familial dysautonomia	Benign (Jan 12, 2018)
9-108867824-T-C		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867834-A-G		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867838-A-C		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867855-G-A		Familial dysautonomia	Benign (Jan 13, 2018)
9-108867856-G-C		Familial dysautonomia	Benign (Jan 13, 2018)
9-108867861-G-T		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867868-A-G		Familial dysautonomia	Likely benign (Jan 13, 2018)
9-108867875-A-G		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867901-G-A		Familial dysautonomia	Uncertain significance (Jan 12, 2018)
9-108867919-C-A		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867921-G-A		Familial dysautonomia	Uncertain significance (Jan 13, 2018)
9-108867924-A-C		Familial dysautonomia	Uncertain significance (Jan 12, 2018)
9-108867991-G-A		Familial dysautonomia	Uncertain significance (Jan 12, 2018)
9-108868044-C-T		Familial dysautonomia	Benign (Jan 13, 2018)
9-108868053-C-A		Familial dysautonomia	Uncertain significance (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELP1	protein_coding	protein_coding	ENST00000374647	36	66600

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.12e-21	1.00	125624	0	124	125748	0.000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0798	698	692	1.01	0.0000369	8763
Missense in Polyphen		253	256.28	0.9872		3324
Synonymous	0.0676	255	256	0.995	0.0000140	2498
Loss of Function	3.54	47	81.5	0.577	0.00000423	957

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00153	0.00153
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000707	0.000707
Finnish	0.0000932	0.0000924
European (Non-Finnish)	0.000467	0.000466
Middle Eastern	0.000707	0.000707
South Asian	0.000523	0.000523
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a scaffold protein that may assemble active IKK-MAP3K14 complexes (IKKA, IKKB and MAP3K14/NIK).
• Disease: DISEASE: Neuropathy, hereditary sensory and autonomic, 3 (HSAN3) [MIM:223900]: A form of hereditary sensory and autonomic neuropathy, a genetically and clinically heterogeneous group of disorders characterized by degeneration of dorsal root and autonomic ganglion cells, and by sensory and/or autonomic abnormalities. HSAN3 patients manifest a variety of symptoms such as alacrima, decreased taste, decreased sensitivity to pain and temperature, vasomotor instability, hypoactive or absent deep tendon reflexes, vomiting crises, and gastrointestinal dysfunction. {ECO:0000269|PubMed:11179008, ECO:0000269|PubMed:11179021}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: EGF-Ncore;Chromatin modifying enzymes;HATs acetylate histones;IL1;Chromatin organization;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.553

Intolerance Scores

• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.18

Haploinsufficiency Scores

• pHI: 0.617
• hipred: Y
• hipred_score: 0.747
• ghis: 0.545

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Elp1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); taste/olfaction phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; digestive/alimentary phenotype; vision/eye phenotype; craniofacial 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: elp1
• Affected structure: intestine
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: tRNA wobble uridine modification;regulation of transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;protein phosphorylation;immune response;positive regulation of cell migration;regulation of protein kinase activity;protein-containing complex assembly
• Cellular component: nucleolus;cytoplasm;cytosol;transcription elongation factor complex;Elongator holoenzyme complex
• Molecular function: RNA polymerase II complex binding;protein binding;phosphorylase kinase regulator activity