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

ENSG00000134759NCBI:55250OMIM:616054HGNC:18248Uniprot:Q6IA86AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Intellectual developmental disorder, autosomal recessive 58ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic21937992; 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
clinvar
16
clinvar
3
clinvar
20
missense
2
clinvar
62
clinvar
8
clinvar
5
clinvar
77
nonsense
1
clinvar
1
clinvar
2
start loss
0
frameshift
1
clinvar
5
clinvar
1
clinvar
7
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
4
2
6
non coding
7
clinvar
3
clinvar
1
clinvar
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)3088497
18-36129959-C-T Inborn genetic diseases Uncertain significance (May 11, 2022)2226489
18-36129964-G-C Inborn genetic diseases Uncertain significance (Dec 06, 2021)2265294
18-36129968-T-C Inborn genetic diseases Uncertain significance (Jun 11, 2024)3275239
18-36129989-G-A Inborn genetic diseases • ELP2-related disorder Conflicting classifications of pathogenicity (Feb 01, 2024)2391742
18-36129995-T-G Inborn genetic diseases Uncertain significance (Mar 19, 2024)3275242
18-36130068-C-G Likely benign (Jul 26, 2018)761471
18-36133273-C-T ELP2-related disorder Likely benign (Aug 12, 2019)3035545
18-36133277-C-T Intellectual disability, autosomal recessive 58 • See cases Conflicting classifications of pathogenicity (Aug 03, 2023)1033375
18-36133278-G-A Inborn genetic diseases Uncertain significance (Jun 04, 2024)3275241
18-36133311-A-G Inborn genetic diseases • Intellectual disability, autosomal recessive 58 Uncertain significance (Nov 09, 2021)2373129
18-36133317-G-GT Inborn genetic diseases Uncertain significance (Feb 26, 2022)2272614
18-36136313-C-G ELP2-related disorder Conflicting classifications of pathogenicity (Apr 21, 2023)710518
18-36138270-C-CT Intellectual disability, profound • Intellectual disability, autosomal recessive 58 Conflicting classifications of pathogenicity (Mar 19, 2024)1012186
18-36138316-C-T Inborn genetic diseases Uncertain significance (Oct 13, 2023)3088507
18-36138356-A-C ELP2-related disorder Likely benign (Jun 01, 2024)745201
18-36138371-C-G Inborn genetic diseases Uncertain significance (Mar 22, 2021)2229541
18-36138378-G-A Inborn genetic diseases Uncertain significance (Apr 05, 2023)2532882
18-36138399-C-T Intellectual disability, autosomal recessive 58 Pathogenic (May 17, 2024)3336513
18-36138400-G-A Inborn genetic diseases Uncertain significance (Jun 04, 2021)2230672
18-36138426-G-T Intellectual disability, autosomal recessive 58 Uncertain significance (Aug 03, 2023)2441215
18-36138803-C-A Intellectual disability, autosomal recessive 58 Uncertain significance (Jun 07, 2022)1339828
18-36138846-G-A Inborn genetic diseases Uncertain significance (Aug 02, 2021)2393189
18-36139409-G-A Benign (Dec 31, 2019)780172
18-36139412-T-G Likely benign (Dec 31, 2019)733510

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ELP2protein_codingprotein_codingENST00000442325 2348503
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.18e-200.85012562401241257480.000493
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5754194530.9240.00002195824
Missense in Polyphen102132.130.771941709
Synonymous0.01511621620.9980.000008391668
Loss of Function2.304059.10.6770.00000308642

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001890.00189
Ashkenazi Jewish0.00009920.0000992
East Asian0.0001660.000163
Finnish0.00004620.0000462
European (Non-Finnish)0.0005120.000510
Middle Eastern0.0001660.000163
South Asian0.0005240.000523
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Elp2
Phenotype

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