ERCC6L2

ERCC excision repair 6 like 2

Basic information

Region (hg38): 9:95871264-96121154

Previous symbols: [ "C9orf102" ]

Links

ENSG00000182150NCBI:375748OMIM:615667HGNC:26922Uniprot:Q5T890AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • pancytopenia-developmental delay syndrome (Definitive), mode of inheritance: AR
  • pancytopenia-developmental delay syndrome (Supportive), mode of inheritance: AR
  • pancytopenia-developmental delay syndrome (Strong), mode of inheritance: AR
  • pancytopenia-developmental delay syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Bone marrow failure syndrome 2ARHematologicIndividuals have been described with tri-lineage bone marrow failure, and awareness may allow prompt recognition and management related to hematologic (eg, anemia) and infectious sequelaeHematologic; Neurologic24507776

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ERCC6L2 gene.

  • not_provided (864 variants)
  • Inborn_genetic_diseases (714 variants)
  • Pancytopenia-developmental_delay_syndrome (39 variants)
  • ERCC6L2-related_disorder (38 variants)
  • not_specified (31 variants)
  • Bone_marrow_hypocellularity (3 variants)
  • Thrombocytopenia (1 variants)
  • Pancytopenia (1 variants)
  • Hereditary_cancer-predisposing_syndrome (1 variants)
  • Growth_hormone_insensitivity_with_immune_dysregulation_1,_autosomal_recessive (1 variants)
  • Premature_ovarian_insufficiency (1 variants)
  • Hereditary_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERCC6L2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020207.7. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
357
clinvar
2
clinvar
361
missense
2
clinvar
811
clinvar
30
clinvar
8
clinvar
851
nonsense
11
clinvar
3
clinvar
14
start loss
0
frameshift
19
clinvar
10
clinvar
7
clinvar
36
splice donor/acceptor (+/-2bp)
1
clinvar
6
clinvar
7
Total 31 21 820 387 10

Highest pathogenic variant AF is 0.00027972

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ERCC6L2protein_codingprotein_codingENST00000288985 14138860
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.06e-71.0012556411831257480.000732
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6363343680.9070.00001824661
Missense in Polyphen86137.190.626891719
Synonymous-0.8491411291.100.000006341344
Loss of Function3.131737.70.4500.00000215458

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003340.000334
Ashkenazi Jewish0.000.00
East Asian0.0003960.000381
Finnish0.005250.00519
European (Non-Finnish)0.0004570.000440
Middle Eastern0.0003960.000381
South Asian0.00009830.0000980
Other0.0004940.000489

dbNSFP

Source: dbNSFP

Function
FUNCTION: May be involved in early DNA damage response. {ECO:0000269|PubMed:24507776}.;
Disease
DISEASE: Bone marrow failure syndrome 2 (BMFS2) [MIM:615715]: An autosomal recessive disorder characterized by trilineage bone marrow failure, bone marrow hypocellularity, learning difficulties, and microcephaly. Insufficient hematopoiesis results in peripheral blood cytopenias, affecting myeloid, erythroid and megakaryocyte lines. Cutaneous features and increased chromosome breakage are not features. {ECO:0000269|PubMed:24507776}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.0840

Haploinsufficiency Scores

pHI
0.0622
hipred
N
hipred_score
0.379
ghis
0.458

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerHighMediumHigh

Mouse Genome Informatics

Gene name
Ercc6l2
Phenotype

Gene ontology

Biological process
cellular response to reactive oxygen species;interstrand cross-link repair
Cellular component
nucleus;cytoplasm;mitochondrion;centrosome;protein-containing complex
Molecular function
DNA binding;helicase activity;ATP binding;protein kinase binding