RAD54L2

RAD54 like 2

Basic information

Region (hg38): 3:51538718-51668667

Links

ENSG00000164080 ∙ NCBI:23132 ∙ OMIM:620006 ∙ HGNC:29123 ∙ Uniprot:Q9Y4B4 ∙ 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 RAD54L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAD54L2 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					5	5
missense			66	5		71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	66	5	5

Variants in RAD54L2

This is a list of pathogenic ClinVar variants found in the RAD54L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-51590511-G-A		not specified	Uncertain significance (Jan 17, 2024)
3-51627615-C-T		not specified	Uncertain significance (Jun 23, 2021)
3-51627667-T-C		not specified	Uncertain significance (Jun 13, 2023)
3-51627673-G-A		not specified	Likely benign (Aug 20, 2023)
3-51627761-T-C			Benign (Mar 02, 2018)
3-51629344-C-T		not specified	Uncertain significance (Jun 29, 2023)
3-51629347-G-C		not specified	Uncertain significance (Jun 28, 2023)
3-51629437-G-A		not specified	Uncertain significance (Sep 20, 2023)
3-51630337-A-G		not specified	Uncertain significance (May 09, 2023)
3-51630746-A-G		not specified	Uncertain significance (Oct 06, 2021)
3-51630831-G-A		not specified	Uncertain significance (Dec 17, 2021)
3-51633577-A-G		not specified	Uncertain significance (Mar 19, 2024)
3-51633588-C-G		not specified	Uncertain significance (Aug 21, 2023)
3-51633951-C-T		not specified	Uncertain significance (Feb 06, 2024)
3-51633966-C-T		not specified	Uncertain significance (Oct 30, 2023)
3-51633971-G-A		not specified	Uncertain significance (Apr 13, 2022)
3-51633976-C-G		not specified	Uncertain significance (Jan 18, 2023)
3-51634017-T-C		not specified	Uncertain significance (Dec 22, 2023)
3-51635595-C-T		not specified	Uncertain significance (Nov 21, 2023)
3-51635597-A-G		not specified	Uncertain significance (Jul 19, 2023)
3-51635667-T-G		not specified	Uncertain significance (Feb 15, 2023)
3-51637240-C-G			Benign (Mar 02, 2018)
3-51637275-G-A		not specified	Uncertain significance (Apr 15, 2024)
3-51637370-C-T		not specified	Uncertain significance (Jan 26, 2022)
3-51637371-G-A		not specified	Uncertain significance (Apr 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAD54L2	protein_coding	protein_coding	ENST00000409535	21	127524

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	6.81e-10	125581	0	3	125584	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.13	592	849	0.698	0.0000506	9554
Missense in Polyphen		119	288.67	0.41224		3201
Synonymous	2.06	283	331	0.856	0.0000193	2975
Loss of Function	7.20	1	62.4	0.0160	0.00000350	715

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000892	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.0000349	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA helicase that modulates androgen receptor (AR)- dependent transactivation in a promoter-dependent manner. Not able to remodel mononucleosomes in vitro (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0931

Intolerance Scores

• rvis_EVS: -1.39
• rvis_percentile_EVS: 4.31

Haploinsufficiency Scores

• pHI: 0.999
• hipred: Y
• hipred_score: 0.786
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.758

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rad54l2
• 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); embryo 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); growth/size/body region phenotype; cellular phenotype

Gene ontology

• Cellular component: nucleus
• Molecular function: DNA binding;helicase activity;protein binding;ATP binding