PHF21A

PHD finger protein 21A, the group of PHD finger proteins

Basic information

Region (hg38): 11:45929319-46121454

Links

ENSG00000135365

∙ NCBI:51317 ∙ OMIM:608325 ∙ HGNC:24156 ∙ Uniprot:Q96BD5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Potocki-Shaffer syndrome (Strong), mode of inheritance: AD
intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures (Moderate), mode of inheritance: AD
intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures (Strong), mode of inheritance: AD
complex neurodevelopmental disorder (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	30487643; 31649809

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PHF21A gene.

not_provided (261 variants)
Inborn_genetic_diseases (61 variants)
Intellectual_developmental_disorder_with_behavioral_abnormalities_and_craniofacial_dysmorphism_with_or_without_seizures (38 variants)
PHF21A-related_disorder (18 variants)
not_specified (9 variants)
See_cases (3 variants)
Autism_spectrum_disorder (1 variants)
Intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF21A gene is commonly pathogenic or not. These statistics are base on transcript: NM_001352027.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	60 clinvar	7 clinvar	69
missense	2 clinvar		121 clinvar	23 clinvar	13 clinvar	159
nonsense	8 clinvar	4 clinvar				12
start loss						0
frameshift	17 clinvar	4 clinvar	2 clinvar			23
splice donor/acceptor (+/-2bp)		6 clinvar	1 clinvar	1 clinvar		8
Total	27	14	126	84	20

Highest pathogenic variant AF is 0.00000479439

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF21A	protein_coding	protein_coding	ENST00000418153	16	192115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000170	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.86	223	380	0.587	0.0000201	4444
Missense in Polyphen		68	153.12	0.44411		1865
Synonymous	1.17	124	142	0.875	0.00000789	1366
Loss of Function	5.64	0	37.1	0.00	0.00000192	395

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

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it may act as a scaffold. Inhibits KDM1A-mediated demethylation of 'Lys-4' of histone H3 in vitro, suggesting a role in demethylation regulation. {ECO:0000269|PubMed:16140033}.;
Pathway: Factors involved in megakaryocyte development and platelet production;HDACs deacetylate histones;Chromatin modifying enzymes;Hemostasis;Chromatin organization (Consensus)

Recessive Scores

pRec: 0.131

Intolerance Scores

loftool: 0.0517
rvis_EVS: -0.62
rvis_percentile_EVS: 17.31

Haploinsufficiency Scores

pHI: 0.459
hipred: Y
hipred_score: 0.853
ghis: 0.611

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: H
gene_indispensability_pred: E
gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Phf21a
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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Zebrafish Information Network

Gene name: phf21ab
Affected structure: aortic arch
Phenotype tag: abnormal
Phenotype quality: hypoplastic

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;blood coagulation;histone deacetylation
Cellular component: histone deacetylase complex;nucleoplasm;DNA repair complex
Molecular function: DNA binding;chromatin binding;histone deacetylase activity;protein binding;metal ion binding