RAD54L

RAD54 like

Basic information

Region (hg38): 1:46246460-46278480

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.

• Inborn genetic diseases (803 variants)
• Hereditary breast ovarian cancer syndrome (37 variants)
• Familial cancer of breast (7 variants)
• Non-Hodgkin lymphoma (3 variants)
• Premature ovarian failure (3 variants)
• not provided (2 variants)
• not specified (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.

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				276	1	277
missense		4	484	40	1	529
nonsense			1			1
start loss						0
frameshift		1	2			3
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region				5		5
non coding				13	2	15
Total	0	5	489	329	4

Highest pathogenic variant AF is 0.0000395

Variants in RAD54L

This is a list of pathogenic ClinVar variants found in the RAD54L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-46248513-G-C		not specified	Uncertain significance (May 24, 2022)
1-46248514-G-A		not specified	Likely benign (Jul 27, 2023)
1-46248514-G-T		not specified	Uncertain significance (Jan 15, 2022)
1-46248515-A-T		not specified	Uncertain significance (Aug 25, 2023)
1-46248516-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-46248517-G-A		not specified	Likely benign (Jan 06, 2023)
1-46248517-G-C		not specified	Uncertain significance (Apr 02, 2022)
1-46248519-G-T		not specified	Uncertain significance (Feb 09, 2024)
1-46248521-T-C		not specified	Likely benign (Apr 06, 2023)
1-46248522-T-C		not specified	Uncertain significance (Jan 05, 2022)
1-46248523-G-A		not specified	Likely benign (Aug 31, 2023)
1-46248530-A-C		not specified	Uncertain significance (May 24, 2022)
1-46248532-C-G		not specified	Uncertain significance (Jun 28, 2023)
1-46248534-A-G		not specified	Uncertain significance (Aug 30, 2023)
1-46248535-G-C		not specified	Uncertain significance (Mar 20, 2022)
1-46248535-G-T		not specified	Uncertain significance (Dec 24, 2023)
1-46248536-C-G		not specified	Uncertain significance (Jan 18, 2023)
1-46248538-G-A		not specified	Likely benign (Sep 13, 2023)
1-46248541-C-T		not specified	Likely benign (Apr 30, 2023)
1-46248544-G-C		not specified	Uncertain significance (Jan 11, 2024)
1-46248546-G-A		not specified	Uncertain significance (Jan 01, 2022)
1-46248552-C-T		not specified	Uncertain significance (Mar 14, 2024)
1-46248553-T-C		not specified	Likely benign (Feb 12, 2022)
1-46248556-A-G		not specified	Likely benign (Mar 07, 2022)
1-46248557-G-A		not specified	Uncertain significance (Aug 11, 2021)

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