PHF3

PHD finger protein 3, the group of PHD finger proteins

Basic information

Region (hg38): 6:63635802-63779336

Links

ENSG00000118482 ∙ NCBI:23469 ∙ OMIM:607789 ∙ HGNC:8921 ∙ Uniprot:Q92576 ∙ 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 PHF3 gene.

• not_specified (228 variants)
• PHF3-related_disorder (47 variants)
• not_provided (15 variants)
• Neurodevelopmental_disorder (1 variants)
• Autism_spectrum_disorder (1 variants)
• Neurodevelopmental_delay (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 PHF3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001370348.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				14	2	16
missense			221	24	10	255
nonsense			2			2
start loss						0
frameshift			2			2
splice donor/acceptor (+/-2bp)						0
Total	0	0	225	38	12

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF3	protein_coding	protein_coding	ENST00000262043	15	143505

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00744	125712	0	34	125746	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.755	972	1.04e+3	0.934	0.0000514	13568
Missense in Polyphen		237	364.37	0.65044		4667
Synonymous	-1.04	383	358	1.07	0.0000178	3747
Loss of Function	6.78	15	80.8	0.186	0.00000453	1074

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000252	0.000246
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000110	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000161	0.000158
Middle Eastern	0.000110	0.000109
South Asian	0.000247	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0921

Intolerance Scores

• loftool: 0.272
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.1

Haploinsufficiency Scores

• pHI: 0.691
• hipred: N
• hipred_score: 0.342
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phf3

Gene ontology

• Biological process: transcription, DNA-templated;multicellular organism development
• Cellular component: cellular_component
• Molecular function: molecular_function;metal ion binding