PHF3

PHD finger protein 3, the group of PHD finger proteins

Basic information

Region (hg38): 6:63635801-63779336

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 provided (402 variants)
• Retinitis pigmentosa 25 (118 variants)
• Inborn genetic diseases (79 variants)
• Retinitis pigmentosa (45 variants)
• Retinal dystrophy (18 variants)
• Autosomal recessive retinitis pigmentosa (14 variants)
• not specified (13 variants)
• PHF3-related condition (7 variants)
• Retinitis Pigmentosa, Recessive (4 variants)
• EYS-related condition (2 variants)
• 7 conditions (1 variants)
• Neurodevelopmental disorder (1 variants)
• Neurodevelopmental delay (1 variants)
• Autism spectrum disorder (1 variants)
• Intellectual disability (1 variants)
• Color vision defect;Retinal dystrophy;Visual impairment;Horizontal nystagmus (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.

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				3		3
missense			65	9	4	78
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding	66	58	174	132		430
Total	66	58	241	144	4

Highest pathogenic variant AF is 0.0000197

Variants in PHF3

This is a list of pathogenic ClinVar variants found in the PHF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-63646657-G-A		not specified	Likely benign (Apr 07, 2023)
6-63646702-G-A		PHF3-related disorder	Uncertain significance (Nov 22, 2022)
6-63646802-C-A		PHF3-related disorder	Likely benign (Dec 06, 2019)
6-63646806-CT-C			Benign (Jan 02, 2024)
6-63680067-A-T		not specified	Uncertain significance (Dec 16, 2022)
6-63684119-CCT-C		PHF3-related disorder	Benign (Sep 05, 2019)
6-63684165-A-G			Benign (Jun 08, 2018)
6-63684176-G-T		PHF3-related disorder	Benign (Jun 06, 2019)
6-63684213-A-G		not specified	Uncertain significance (Dec 15, 2023)
6-63684220-A-G		PHF3-related disorder	Benign (Jun 15, 2021)
6-63684224-A-G		not specified	Likely benign (Nov 21, 2023)
6-63684419-G-A		PHF3-related disorder	Benign (Jun 15, 2021)
6-63684440-T-C		not specified	Uncertain significance (Jun 28, 2023)
6-63684459-T-C		not specified	Uncertain significance (Jan 22, 2024)
6-63684465-T-G		not specified	Uncertain significance (May 24, 2023)
6-63684483-A-C		not specified	Likely benign (Jul 20, 2021)
6-63684546-A-G		not specified	Uncertain significance (Dec 12, 2022)
6-63684574-A-G		PHF3-related disorder	Likely benign (Dec 18, 2023)
6-63684639-A-C		not specified	Uncertain significance (Sep 14, 2022)
6-63684668-A-G		not specified	Likely benign (Dec 22, 2023)
6-63684684-A-G		PHF3-related disorder	Uncertain significance (Dec 29, 2023)
6-63684737-G-T		not specified	Uncertain significance (Apr 12, 2022)
6-63684855-A-G		not specified	Likely benign (Apr 12, 2023)
6-63684936-C-T		not specified	Conflicting classifications of pathogenicity (Apr 01, 2022)
6-63684951-A-T		not specified	Uncertain significance (Aug 30, 2022)

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