RAD54L

RAD54 like

Basic information

Region (hg38): 1:46246461-46278480

Links

ENSG00000085999

∙ NCBI:8438 ∙ OMIM:603615 ∙ HGNC:9826 ∙ Uniprot:Q92698 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAD54L gene.

not_specified (1041 variants)
Hereditary_breast_ovarian_cancer_syndrome (36 variants)
not_provided (17 variants)
Familial_cancer_of_breast (11 variants)
RAD54L-related_disorder (9 variants)
Non-Hodgkin_lymphoma (4 variants)
Premature_ovarian_failure (3 variants)
Inborn_genetic_diseases (2 variants)
Colon_adenocarcinoma (1 variants)
Lymphoma,_non-Hodgkin,_familial (1 variants)
Autosomal_dominant_hypophosphatemic_rickets (1 variants)
Hereditary_diffuse_gastric_adenocarcinoma (1 variants)
Breast_ductal_adenocarcinoma (1 variants)
Astrocytoma_IDH-mutant (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAD54L gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003579.4. 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				334 clinvar		334
missense	3 clinvar	5 clinvar	662 clinvar	52 clinvar		722
nonsense		1 clinvar	1 clinvar			2
start loss						0
frameshift		1 clinvar	3 clinvar			4
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	3	7	667	386	0

Highest pathogenic variant AF is 0.000108423

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAD54L	protein_coding	protein_coding	ENST00000371975	18	30786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.36e-15	0.594	125448	2	298	125748	0.00119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.252	424	410	1.04	0.0000267	4883
Missense in Polyphen		187	171.12	1.0928		2060
Synonymous	-0.268	158	154	1.03	0.00000846	1475
Loss of Function	1.71	29	40.8	0.711	0.00000257	456

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00125	0.00124
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00436	0.00419
Finnish	0.000281	0.000277
European (Non-Finnish)	0.000671	0.000659
Middle Eastern	0.00436	0.00419
South Asian	0.00345	0.00334
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in DNA repair and mitotic recombination. Functions in the recombinational DNA repair (RAD52) pathway. Dissociates RAD51 from nucleoprotein filaments formed on dsDNA. Could be involved in the turnover of RAD51 protein-dsDNA filaments (By similarity). May play also an essential role in telomere length maintenance and telomere capping in mammalian cells. {ECO:0000250, ECO:0000269|PubMed:11459989, ECO:0000269|PubMed:12205100, ECO:0000269|PubMed:9774452}.;
Pathway: Homologous recombination - Homo sapiens (human);Integrated Breast Cancer Pathway (Consensus)

Recessive Scores

pRec: 0.148

Intolerance Scores

loftool: 0.160
rvis_EVS: -0.37
rvis_percentile_EVS: 28.2

Haploinsufficiency Scores

pHI: 0.831
hipred: Y
hipred_score: 0.617
ghis: 0.640

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.576

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Rad54l
Phenotype: hematopoietic system 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); homeostasis/metabolism phenotype; cellular phenotype;

Gene ontology

Biological process: double-strand break repair via homologous recombination;DNA strand renaturation;DNA repair;DNA recombination;determination of adult lifespan;response to ionizing radiation;response to drug;meiotic cell cycle
Cellular component: nucleus;nucleoplasm;protein-containing complex
Molecular function: DNA binding;helicase activity;protein binding;ATP binding;annealing helicase activity