YAF2

YY1 associated factor 2, the group of Zinc fingers RANBP2-type

Basic information

Region (hg38): 12:42157103-42238349

Links

ENSG00000015153 ∙ NCBI:10138 ∙ OMIM:607534 ∙ HGNC:17363 ∙ Uniprot:Q8IY57 ∙ 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 YAF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YAF2 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	11	1	0

Variants in YAF2

This is a list of pathogenic ClinVar variants found in the YAF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-42160620-T-C		not specified	Uncertain significance (May 31, 2022)
12-42160638-G-A		not specified	Uncertain significance (Nov 08, 2022)
12-42160645-A-G		not specified	Uncertain significance (Jul 20, 2022)
12-42160678-C-T		not specified	Uncertain significance (Oct 31, 2023)
12-42160752-A-G		not specified	Uncertain significance (Mar 06, 2023)
12-42161655-T-A		not specified	Uncertain significance (May 26, 2024)
12-42210599-A-G		not specified	Uncertain significance (Nov 18, 2022)
12-42210608-A-G		not specified	Uncertain significance (Oct 06, 2021)
12-42235898-C-T			Likely benign (Apr 01, 2023)
12-42237632-A-G		not specified	Uncertain significance (Jun 13, 2023)
12-42237651-C-G		not specified	Uncertain significance (Dec 15, 2023)
12-42237690-C-T		not specified	Uncertain significance (May 11, 2022)
12-42237698-G-A		not specified	Uncertain significance (Apr 15, 2024)
12-42238158-G-A		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YAF2	protein_coding	protein_coding	ENST00000442791	5	81246

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.795	0.204	125524	0	1	125525	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	57	101	0.563	0.00000488	1319
Missense in Polyphen		16	42.024	0.38073		563
Synonymous	0.750	32	37.9	0.845	0.00000197	370
Loss of Function	2.57	1	9.60	0.104	4.72e-7	126

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)	0.00000881	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to MYC and inhibits MYC-mediated transactivation. Also binds to MYCN and enhances MYCN-dependent transcriptional activation. Increases calpain 2-mediated proteolysis of YY1 in vitro. Component of the E2F6.com-1 complex, a repressive complex that methylates 'Lys-9' of histone H3, suggesting that it is involved in chromatin-remodeling. {ECO:0000269|PubMed:11593398, ECO:0000269|PubMed:12706874, ECO:0000269|PubMed:9016636}.
• Pathway: Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Transcriptional Regulation by E2F6;Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.108

Haploinsufficiency Scores

• pHI: 0.168
• hipred: Y
• hipred_score: 0.816
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.919

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Yaf2

Gene ontology

• Biological process: negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;negative regulation of G0 to G1 transition
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: transcription coactivator activity;transcription corepressor activity;protein binding;metal ion binding