YY1AP1

protein-coding

YY1 associated protein 1

Gene summary

Involved in cell differentiation; cell population proliferation; and regulation of cell cycle. Located in Ino80 complex; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_139119.3

Inheritance

AD, AR

ClinVar variants

P:11U:120B:37

Top phenotype

Grange syndrome

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr1:155,659,446-155,689,334

External References & Databases

Ensembl (ENSG00000163374)

Transcript & Mutation Effects

hg38 • Region Span ~29.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

grange syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011243

Submitter: Orphanet

grange syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011243

Submitter: PanelApp Australia

grange syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011243

Submitter: Genomics England PanelApp

grange syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0011243

Submitter: Ambry Genetics

grange syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011243

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Grange syndromeAR

Manifestation: Cardiovascular; Craniofacial; Musculoskeletal; Neurologic

Intervention: Cardiovascular

Rationale: Among other features, individuals have been described with arrhythmias and vascular anomalies, and awareness may allow early diagnosis and management of these issues

Refs: 9489789; 11241488; 16691574; 27939641; 30556293

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to YY1AP1 variants in ClinVar

5 Conditions Cataloged

Inborn genetic diseasesTotal: 142

not providedTotal: 34

Grange syndromeTotal: 17

YY1AP1-related disorderTotal: 17

not specifiedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_139119.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	17 clinvar	2 clinvar	20
missense			112 clinvar	14 clinvar	4 clinvar	130
nonsense	3 clinvar	1 clinvar				4
start loss			1 clinvar			1
frameshift		4 clinvar	4 clinvar			8
splice donor/acceptor (+/-2bp)	1 clinvar	2 clinvar	2 clinvar			5
Total	4	7	120	31	6	168

Highest pathogenic variant AF is 0.000029811961

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 185 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_139119.3	RefSeq	NP_620830.1	9	MANE Select
ENST00000355499.9	Ensembl	ENSP00000347686.4	9	MANE Select
NM_001198899.2	RefSeq	NP_001185828.1	8	Standard
NM_001198900.2	RefSeq	NP_001185829.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell population proliferation
cell differentiation
regulation of cell cycle

Molecular Function

protein binding

Cellular Component

fibrillar center
nucleus
nucleoplasm
nucleolus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368339
Coding exons: 10
Length: 29555
Individuals with no LoFs: 125662
Homozygous LoFs: 1
Heterozygous LoFs: 85
Defined: 125748
p: 0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.18	539	467	1.15	0.0000239	5745
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00038	0.00033	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00050	0.00048	rare
South Asian	0.00023	0.00023	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.727

Gene Damage Prediction

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