ELP2

elongator acetyltransferase complex subunit 2, the group of WD repeat domain containing|Elongator acetyltransferase complex

Basic information

Region (hg38): 18:36129444-36180557

Previous symbols: [ "STATIP1" ]

Links

ENSG00000134759 ∙ NCBI:55250 ∙ OMIM:616054 ∙ HGNC:18248 ∙ Uniprot:Q6IA86 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, autosomal recessive 58 (Moderate), mode of inheritance: AR
• intellectual disability, autosomal recessive 58 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 58	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	Neurologic	21937992; 25847581

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ELP2 gene.

• Inborn genetic diseases (1 variants)
• Intellectual disability, autosomal recessive 58 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELP2 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			1	16	3	20
missense		2	62	8	5	77
nonsense	1		1			2
start loss						0
frameshift	1	5	1			7
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			4	2		6
non coding			7	3	1	11
Total	2	7	72	27	9

Highest pathogenic variant AF is 0.0000263

Variants in ELP2

This is a list of pathogenic ClinVar variants found in the ELP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-36129943-C-G		Inborn genetic diseases	Uncertain significance (Nov 17, 2023)
18-36129959-C-T		Inborn genetic diseases	Uncertain significance (May 11, 2022)
18-36129964-G-C		Inborn genetic diseases	Uncertain significance (Dec 06, 2021)
18-36129968-T-C		Inborn genetic diseases	Uncertain significance (Jun 11, 2024)
18-36129989-G-A		Inborn genetic diseases • ELP2-related disorder	Conflicting classifications of pathogenicity (Feb 01, 2024)
18-36129995-T-G		Inborn genetic diseases	Uncertain significance (Mar 19, 2024)
18-36130068-C-G			Likely benign (Jul 26, 2018)
18-36133273-C-T		ELP2-related disorder	Likely benign (Aug 12, 2019)
18-36133277-C-T		Intellectual disability, autosomal recessive 58 • See cases	Conflicting classifications of pathogenicity (Aug 03, 2023)
18-36133278-G-A		Inborn genetic diseases	Uncertain significance (Jun 04, 2024)
18-36133311-A-G		Inborn genetic diseases • Intellectual disability, autosomal recessive 58	Uncertain significance (Nov 09, 2021)
18-36133317-G-GT		Inborn genetic diseases	Uncertain significance (Feb 26, 2022)
18-36136313-C-G		ELP2-related disorder	Conflicting classifications of pathogenicity (Apr 21, 2023)
18-36138270-C-CT		Intellectual disability, profound • Intellectual disability, autosomal recessive 58	Conflicting classifications of pathogenicity (Mar 19, 2024)
18-36138316-C-T		Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
18-36138356-A-C		ELP2-related disorder	Likely benign (Jun 01, 2024)
18-36138371-C-G		Inborn genetic diseases	Uncertain significance (Mar 22, 2021)
18-36138378-G-A		Inborn genetic diseases	Uncertain significance (Apr 05, 2023)
18-36138399-C-T		Intellectual disability, autosomal recessive 58	Pathogenic (May 17, 2024)
18-36138400-G-A		Inborn genetic diseases	Uncertain significance (Jun 04, 2021)
18-36138426-G-T		Intellectual disability, autosomal recessive 58	Uncertain significance (Aug 03, 2023)
18-36138803-C-A		Intellectual disability, autosomal recessive 58	Uncertain significance (Jun 07, 2022)
18-36138846-G-A		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)
18-36139409-G-A			Benign (Dec 31, 2019)
18-36139412-T-G			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELP2	protein_coding	protein_coding	ENST00000442325	23	48503

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.18e-20	0.850	125624	0	124	125748	0.000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.575	419	453	0.924	0.0000219	5824
Missense in Polyphen		102	132.13	0.77194		1709
Synonymous	0.0151	162	162	0.998	0.00000839	1668
Loss of Function	2.30	40	59.1	0.677	0.00000308	642

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00189	0.00189
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000166	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000512	0.000510
Middle Eastern	0.000166	0.000163
South Asian	0.000524	0.000523
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates the ligand-dependent activation of STAT3. {ECO:0000250}.
• Disease: DISEASE: Mental retardation, autosomal recessive 58 (MRT58) [MIM:617270]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT58 transmission pattern is consistent with autosomal recessive inheritance. {ECO:0000269|PubMed:25847581}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.867
• rvis_EVS: 1.21
• rvis_percentile_EVS: 93.02

Haploinsufficiency Scores

• pHI: 0.471
• hipred: Y
• hipred_score: 0.538
• ghis: 0.519

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.778

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elp2

Gene ontology

• Biological process: tRNA wobble uridine modification;regulation of transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;regulation of JAK-STAT cascade
• Cellular component: cytoplasm;cytosol;transcription elongation factor complex;Elongator holoenzyme complex
• Molecular function: RNA polymerase II complex binding;protein kinase binding