YY1AP1

YY1 associated protein 1

Basic information

Region (hg38): 1:155659446-155689334

Links

ENSG00000163374 ∙ NCBI:55249 ∙ OMIM:607860 ∙ HGNC:30935 ∙ Uniprot:Q9H869 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• grange syndrome (Strong), mode of inheritance: AR
• grange syndrome (Strong), mode of inheritance: AR
• grange syndrome (Supportive), mode of inheritance: AD
• grange syndrome (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Grange syndrome	AR	Cardiovascular	Among other features, individuals have been described with arrhythmias and vascular anomalies, and awareness may allow early diagnosis and management of these issues	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic	9489789; 11241488; 16691574; 27939641; 30556293

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the YY1AP1 gene.

• Grange syndrome (2 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YY1AP1 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				13	4	17
missense			56	12	6	74
nonsense	1	1				2
start loss						0
frameshift	1	2	2			5
inframe indel			1		1	2
splice donor/acceptor (+/-2bp)	1	1				2
splice region				1		1
non coding	1	1	1		1	4
Total	4	5	60	25	12

Highest pathogenic variant AF is 0.0000657

Variants in YY1AP1

This is a list of pathogenic ClinVar variants found in the YY1AP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155659660-A-G		YY1AP1-related disorder	Benign (Feb 09, 2018)
1-155659731-A-G		Inborn genetic diseases	Likely benign (Dec 17, 2023)
1-155659731-A-T		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
1-155659809-T-C		Inborn genetic diseases	Uncertain significance (Apr 03, 2023)
1-155659815-G-A		Inborn genetic diseases	Uncertain significance (May 09, 2022)
1-155659815-G-T		Inborn genetic diseases	Uncertain significance (Jun 14, 2023)
1-155659823-C-T		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
1-155659837-T-C		YY1AP1-related disorder	Likely benign (Oct 19, 2023)
1-155659857-C-T		Inborn genetic diseases	Uncertain significance (Jun 02, 2023)
1-155659923-C-A		Grange syndrome	Pathogenic (Feb 14, 2017)
1-155659934-A-T		Grange syndrome	Pathogenic (Feb 14, 2017)
1-155659961-T-C		Inborn genetic diseases	Uncertain significance (May 22, 2023)
1-155659971-C-T		Inborn genetic diseases	Likely benign (Dec 14, 2021)
1-155660001-T-C		Inborn genetic diseases	Likely benign (Jun 23, 2021)
1-155660087-A-G		Inborn genetic diseases	Uncertain significance (Jan 06, 2023)
1-155660137-G-A		YY1AP1-related disorder	Likely benign (Dec 31, 2019)
1-155660148-T-C		Inborn genetic diseases	Uncertain significance (Jun 21, 2023)
1-155660155-G-A			Likely benign (Nov 01, 2023)
1-155660173-C-T			Benign (Dec 31, 2019)
1-155660177-T-C		Inborn genetic diseases	Likely benign (Oct 06, 2023)
1-155660191-C-T			Benign (Dec 31, 2019)
1-155660202-C-T		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
1-155660267-A-G		Inborn genetic diseases	Uncertain significance (May 05, 2023)
1-155660328-G-A		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)
1-155660382-T-C		Inborn genetic diseases	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YY1AP1	protein_coding	protein_coding	ENST00000368339	10	29555

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.95e-18	0.00677	125662	1	85	125748	0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.18	539	467	1.15	0.0000239	5745
Missense in Polyphen		144	126.43	1.139		1816
Synonymous	-1.98	216	182	1.19	0.00000903	1855
Loss of Function	0.227	28	29.3	0.955	0.00000133	369

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000422	0.000420
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000381	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000495	0.000484
Middle Eastern	0.000381	0.000326
South Asian	0.000235	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with the INO80 chromatin remodeling complex, which is responsible for transcriptional regulation, DNA repair, and replication (PubMed:27939641). Enhances transcription activation by YY1 (PubMed:14744866). Plays a role in cell cycle regulation (PubMed:17541814, PubMed:27939641). {ECO:0000269|PubMed:14744866, ECO:0000269|PubMed:17541814, ECO:0000269|PubMed:27939641}.

Recessive Scores

• pRec: 0.0801

Intolerance Scores

• loftool: 0.942
• rvis_EVS: 0.52
• rvis_percentile_EVS: 80.34

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.273
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.727

Gene Damage Prediction

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

Gene ontology

• Biological process: cell population proliferation;cell differentiation;regulation of cell cycle
• Cellular component: fibrillar center;nucleus;nucleoplasm;nucleolus;cytoplasm;Ino80 complex
• Molecular function: protein binding