YJU2

YJU2 splicing factor homolog

Basic information

Region (hg38): 19:4247079-4269088

Previous symbols: [ "CCDC94" ]

Links

ENSG00000105248 ∙ NCBI:55702 ∙ ∙ HGNC:25518 ∙ Uniprot:Q9BW85 ∙ 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 YJU2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YJU2 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					1	1
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	1

Variants in YJU2

This is a list of pathogenic ClinVar variants found in the YJU2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4249256-C-T		not specified	Uncertain significance (Aug 10, 2021)
19-4251124-C-T		not specified	Uncertain significance (Dec 14, 2021)
19-4251139-T-C		not specified	Uncertain significance (May 06, 2024)
19-4254383-T-G		not specified	Uncertain significance (Apr 09, 2024)
19-4254468-G-C		not specified	Uncertain significance (Aug 13, 2021)
19-4258300-A-G		not specified	Uncertain significance (May 17, 2023)
19-4258319-C-A		not specified	Uncertain significance (Jul 30, 2023)
19-4258347-G-T		not specified	Uncertain significance (Aug 04, 2023)
19-4258372-C-T		not specified	Uncertain significance (Aug 16, 2021)
19-4258384-G-A		not specified	Uncertain significance (Nov 10, 2022)
19-4258387-G-A		not specified	Likely benign (Nov 21, 2023)
19-4258418-G-C		not specified	Uncertain significance (Mar 11, 2024)
19-4258422-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-4262020-G-A		not specified	Uncertain significance (Dec 03, 2021)
19-4262039-C-T			Benign (May 15, 2018)
19-4262065-C-T		not specified	Uncertain significance (May 24, 2023)
19-4262085-C-T		not specified	Uncertain significance (Apr 20, 2024)
19-4262086-G-A		not specified	Uncertain significance (Jul 27, 2022)
19-4267669-G-A		not specified	Uncertain significance (Mar 29, 2024)
19-4267708-G-A		not specified	Uncertain significance (Sep 28, 2022)
19-4267727-C-G		not specified	Uncertain significance (Aug 23, 2021)
19-4267732-C-T		not specified	Uncertain significance (Jun 12, 2023)
19-4267733-C-G		not specified	Uncertain significance (Apr 08, 2024)
19-4267747-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-4267760-C-T		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YJU2	protein_coding	protein_coding	ENST00000262962	8	22012

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.25e-7	0.754	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	142	203	0.699	0.0000129	2087
Missense in Polyphen		31	63.037	0.49178		710
Synonymous	-0.0510	89	88.4	1.01	0.00000593	610
Loss of Function	1.27	12	17.8	0.676	9.39e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000316	0.000308
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000638	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000838	0.0000791
Middle Eastern	0.0000638	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of the catalytic step I spliceosome, C complex (PubMed:29301961). May protect cells from TP53-dependent apoptosis upon dsDNA break damage through association with PRP19-CD5L complex (PubMed:22952453). {ECO:0000269|PubMed:22952453, ECO:0000269|PubMed:29301961}.

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.0972
• hipred: Y
• hipred_score: 0.629
• ghis: 0.581

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Yju2
• Phenotype: skeleton phenotype; limbs/digits/tail phenotype; vision/eye 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); pigmentation phenotype

Zebrafish Information Network

• Gene name: yju2
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curved

Gene ontology

• Biological process: mRNA processing;RNA splicing;negative regulation of DNA damage response, signal transduction by p53 class mediator
• Cellular component: U2-type catalytic step 1 spliceosome
• Molecular function: protein binding