YJU2B

YJU2 splicing factor homolog B, the group of NTC associated proteins

Basic information

Region (hg38): 19:13731760-13763296

Previous symbols: [ "CCDC130" ]

Links

ENSG00000104957 ∙ NCBI:81576 ∙ ∙ HGNC:28118 ∙ Uniprot:P13994 ∙ 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 YJU2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YJU2B 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			31	2		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	0

Variants in YJU2B

This is a list of pathogenic ClinVar variants found in the YJU2B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-13756243-G-A		not specified	Uncertain significance (Apr 30, 2025)
19-13756269-C-T		not specified	Uncertain significance (Mar 20, 2024)
19-13756272-A-G		not specified	Uncertain significance (May 23, 2023)
19-13757432-A-T		not specified	Uncertain significance (Mar 26, 2025)
19-13757446-G-A		not specified	Uncertain significance (Apr 09, 2024)
19-13757464-A-G		not specified	Uncertain significance (Jul 19, 2023)
19-13758873-G-A		not specified	Uncertain significance (Mar 04, 2025)
19-13758902-A-C		not specified	Uncertain significance (Oct 16, 2024)
19-13758905-G-A		not specified	Uncertain significance (Nov 28, 2024)
19-13758932-G-A		not specified	Uncertain significance (Dec 12, 2023)
19-13758953-G-A		not specified	Uncertain significance (May 13, 2025)
19-13758960-G-A		not specified	Uncertain significance (May 11, 2022)
19-13758969-A-G		not specified	Uncertain significance (May 27, 2022)
19-13759111-A-C		not specified	Uncertain significance (Jan 09, 2024)
19-13759166-G-A		not specified	Uncertain significance (Mar 28, 2025)
19-13759213-G-A		not specified	Uncertain significance (Apr 25, 2022)
19-13762323-G-A		not specified	Uncertain significance (May 28, 2024)
19-13762346-G-C		not specified	Uncertain significance (Nov 07, 2024)
19-13762383-G-A		not specified	Uncertain significance (Sep 09, 2024)
19-13762392-G-C		not specified	Uncertain significance (Dec 04, 2024)
19-13762398-C-T		not specified	Uncertain significance (Jul 12, 2023)
19-13762399-G-A		not specified	Uncertain significance (Jun 26, 2024)
19-13762424-C-A		not specified	Uncertain significance (Jan 12, 2024)
19-13762592-T-C		not specified	Uncertain significance (May 04, 2023)
19-13762617-G-A		not specified	Uncertain significance (Sep 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YJU2B	protein_coding	protein_coding	ENST00000586600	9	31537

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00316	0.987	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.528	240	264	0.909	0.0000184	2573
Missense in Polyphen		109	126	0.86506		1172
Synonymous	-0.576	121	113	1.07	0.00000848	755
Loss of Function	2.26	7	17.1	0.410	8.97e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00111	0.00111
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.0945

Intolerance Scores

• loftool: 0.736
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.07

Haploinsufficiency Scores

• pHI: 0.0885
• hipred: Y
• hipred_score: 0.702
• ghis: 0.487

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.571

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc130

Gene ontology

• Biological process: response to virus
• Cellular component: cellular_component
• Molecular function: protein binding