REV3L

REV3 like, DNA directed polymerase zeta catalytic subunit, the group of DNA polymerases

Basic information

Region (hg38): 6:111299028-111483715

Links

ENSG00000009413

∙ NCBI:5980 ∙ OMIM:602776 ∙ HGNC:9968 ∙ Uniprot:O60673 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Mobius syndrome (Limited), mode of inheritance: Unknown
Mobius syndrome (Supportive), mode of inheritance: AD
Mobius syndrome (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the REV3L gene.

Inborn_genetic_diseases (271 variants)
not_provided (113 variants)
REV3L-related_disorder (36 variants)
not_specified (2 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Carcinoma_of_colon (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the REV3L gene is commonly pathogenic or not. These statistics are base on transcript: NM_001372078.1. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				44 clinvar	15 clinvar	59
missense		1 clinvar	253 clinvar	43 clinvar	15 clinvar	312
nonsense			2 clinvar			2
start loss						0
frameshift	1 clinvar		1 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	1	1	256	87	30

Highest pathogenic variant AF is 0.000007663188

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
REV3L	protein_coding	protein_coding	ENST00000358835	32	184685

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.05e-16	125715	0	22	125737	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.47	1315	1.59e+3	0.826	0.0000808	20622
Missense in Polyphen		329	566.28	0.58099		7303
Synonymous	0.556	544	561	0.970	0.0000278	5956
Loss of Function	10.0	9	135	0.0669	0.00000765	1720

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000143	0.000139
European (Non-Finnish)	0.000110	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.0000333	0.0000327
Other	0.000175	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalytic subunit of the DNA polymerase zeta complex, an error-prone polymerase specialized in translesion DNA synthesis (TLS). Lacks an intrinsic 3'-5' exonuclease activity and thus has no proofreading function. {ECO:0000269|PubMed:24449906}.;
Pathway: Fanconi anemia pathway - Homo sapiens (human);DNA Repair;Purine metabolism;Pyrimidine metabolism;Translesion synthesis by REV1;Translesion synthesis by POLK;Translesion synthesis by POLI;Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template;DNA Damage Bypass (Consensus)

Recessive Scores

pRec: 0.195

Intolerance Scores

loftool: 0.218
rvis_EVS: -2.1
rvis_percentile_EVS: 1.55

Haploinsufficiency Scores

pHI: 0.860
hipred: Y
hipred_score: 0.783
ghis: 0.592

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.761

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Rev3l
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); immune system phenotype; embryo 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); 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); hematopoietic system phenotype; neoplasm; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;

Gene ontology

Biological process: DNA-dependent DNA replication;error-prone translesion synthesis;nucleic acid phosphodiester bond hydrolysis
Cellular component: nucleoplasm;nucleolus;zeta DNA polymerase complex
Molecular function: nucleotide binding;DNA binding;DNA-directed DNA polymerase activity;protein binding;3'-5' exonuclease activity;metal ion binding;4 iron, 4 sulfur cluster binding