RBPJL

recombination signal binding protein for immunoglobulin kappa J region like, the group of PTF1 complex

Basic information

Region (hg38): 20:45306839-45317824

Previous symbols: [ "RBPSUHL" ]

Links

ENSG00000124232 ∙ NCBI:11317 ∙ OMIM:616104 ∙ HGNC:13761 ∙ Uniprot:Q9UBG7 ∙ 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 RBPJL gene.

• Inborn genetic diseases (20 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBPJL 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			20		3	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	3

Variants in RBPJL

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

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

Position	Type	Phenotype	Significance	ClinVar
20-45306935-G-A		not specified	Uncertain significance (May 24, 2023)
20-45307662-C-G		Type 2 diabetes mellitus	Benign (-)
20-45308220-G-A		not specified	Uncertain significance (Jul 19, 2023)
20-45308236-C-G		not specified	Uncertain significance (Nov 08, 2022)
20-45309178-T-C		Type 2 diabetes mellitus	Benign (-)
20-45309619-C-A		not specified	Uncertain significance (Jan 24, 2024)
20-45309643-C-T		not specified	Uncertain significance (Jul 20, 2021)
20-45309644-G-A			Benign (Apr 20, 2018)
20-45311637-G-T		not specified	Uncertain significance (Aug 22, 2022)
20-45311650-C-G		not specified	Uncertain significance (Feb 14, 2024)
20-45312291-G-A		not specified	Uncertain significance (Feb 16, 2023)
20-45312305-G-T		not specified	Uncertain significance (Jul 15, 2021)
20-45312312-G-C		not specified	Uncertain significance (Jun 18, 2021)
20-45312354-C-T		not specified	Uncertain significance (Oct 06, 2021)
20-45313533-C-T		not specified	Uncertain significance (May 08, 2023)
20-45313557-G-A		not specified	Uncertain significance (Nov 03, 2023)
20-45313571-T-G		not specified	Uncertain significance (Nov 03, 2022)
20-45314036-T-C		Type 2 diabetes mellitus	Benign (-)
20-45314071-G-A		not specified	Uncertain significance (Oct 26, 2021)
20-45314082-G-A		not specified	Uncertain significance (Jul 11, 2023)
20-45314116-C-T		Type 2 diabetes mellitus	risk factor (-)
20-45314420-G-A		not specified	Uncertain significance (Nov 17, 2022)
20-45314534-G-A		not specified	Uncertain significance (Dec 16, 2023)
20-45314536-C-T		not specified	Uncertain significance (Dec 18, 2023)
20-45316194-C-G		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBPJL	protein_coding	protein_coding	ENST00000343694	12	10313

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.92e-11	0.468	125621	1	126	125748	0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	277	330	0.840	0.0000205	3311
Missense in Polyphen		108	125.05	0.86366		1295
Synonymous	-0.0784	149	148	1.01	0.00000990	1080
Loss of Function	1.23	20	26.9	0.743	0.00000140	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000449	0.000449
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000273	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000508	0.000484
Middle Eastern	0.000273	0.000272
South Asian	0.00171	0.00167
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative transcription factor, which cooperates with EBNA2 to activate transcription. {ECO:0000250}.
• Pathway: Th1 and Th2 cell differentiation - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Notch signaling pathway - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Notch Signaling Pathway;PTF1A related regulatory pathway;Notch Signaling Pathway (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.538
• rvis_EVS: 1
• rvis_percentile_EVS: 90.69

Haploinsufficiency Scores

• pHI: 0.189
• hipred: N
• hipred_score: 0.439
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.393

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbpjl
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype

Gene ontology

• Biological process: signal transduction;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;transcription factor complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;DNA-binding transcription factor activity;sequence-specific DNA binding