RAD21L1

RAD21 cohesin complex component like 1, the group of Kleisins

Basic information

Region (hg38): 20:1226043-1296421

Links

ENSG00000244588 ∙ NCBI:642636 ∙ OMIM:619533 ∙ HGNC:16271 ∙ Uniprot:Q9H4I0 ∙ 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 RAD21L1 gene.

• Inborn genetic diseases (22 variants)
• not provided (3 variants)
• Non-obstructive azoospermia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAD21L1 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						0
missense			19	3	1	23
nonsense	1					1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	1	0	21	3	1

Variants in RAD21L1

This is a list of pathogenic ClinVar variants found in the RAD21L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-1228507-G-T		not specified	Uncertain significance (Sep 21, 2023)
20-1228538-A-T		Non-obstructive azoospermia	Pathogenic (Aug 23, 2021)
20-1228577-G-A		not specified	Uncertain significance (Feb 27, 2023)
20-1231541-C-T		not specified	Uncertain significance (Jan 16, 2024)
20-1231559-C-T		not specified	Uncertain significance (May 27, 2022)
20-1231594-C-T		not specified	Uncertain significance (Dec 18, 2023)
20-1231617-G-A		not specified	Uncertain significance (Sep 29, 2022)
20-1234089-A-G		not specified	Uncertain significance (Feb 10, 2023)
20-1238062-T-C		not specified	Uncertain significance (Aug 08, 2022)
20-1238166-G-A		not specified	Uncertain significance (Sep 20, 2023)
20-1238199-G-A		not specified	Uncertain significance (Dec 21, 2023)
20-1239354-T-A		not specified	Uncertain significance (Jun 14, 2023)
20-1239396-A-G		not specified	Likely benign (Jul 12, 2023)
20-1240320-G-A			Uncertain significance (Mar 31, 2021)
20-1240341-T-A		not specified	Uncertain significance (Mar 14, 2023)
20-1240344-A-G		not specified	Likely benign (Apr 20, 2023)
20-1240423-T-C		not specified	Uncertain significance (Mar 06, 2023)
20-1242729-A-G		not specified	Uncertain significance (Mar 21, 2023)
20-1242778-A-G		not specified	Uncertain significance (Jan 17, 2023)
20-1242793-A-G		not specified	Uncertain significance (Jun 06, 2023)
20-1243104-CA-C			Uncertain significance (Feb 01, 2023)
20-1243175-G-T		not specified	Uncertain significance (Nov 14, 2023)
20-1243191-T-C		not specified	Uncertain significance (Jun 24, 2022)
20-1244070-A-G		not specified	Uncertain significance (Jun 18, 2021)
20-1244118-G-A		not specified	Likely benign (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAD21L1	protein_coding	protein_coding	ENST00000409241	13	70366

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000453	0.992	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	177	237	0.747	0.0000109	3707
Missense in Polyphen		43	72.145	0.59602		1143
Synonymous	1.76	58	77.8	0.746	0.00000351	963
Loss of Function	2.36	13	26.0	0.500	0.00000148	380

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Meiosis-specific component of some cohesin complex required during the initial steps of prophase I in male meiosis. Probably required during early meiosis in males for separation of sister chromatids and homologous chromosomes. Replaces RAD21 in premeiotic S phase (during early stages of prophase I), while RAD21 reappears in later stages of prophase I. Involved in synaptonemal complex assembly, synapsis initiation and crossover recombination between homologous chromosomes during prophase I (By similarity). {ECO:0000250}.

Intolerance Scores

• rvis_EVS: 0.77
• rvis_percentile_EVS: 86.95

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0837

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rad21l
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: double-strand break repair via homologous recombination;double-strand break repair;sister chromatid cohesion;synaptonemal complex assembly;spermatogenesis;fertilization;meiotic cell cycle;meiotic attachment of telomere to nuclear envelope;seminiferous tubule development
• Cellular component: lateral element;nucleus;chromosome;meiotic cohesin complex;nuclear meiotic cohesin complex
• Molecular function: chromatin binding