PHF3

protein-coding

PHD finger protein 3, the group of PHD finger proteins

Gene summary

This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

MANE transcript

NM_001370348.2

Inheritance

—

ClinVar variants

U:273B:57

Top phenotype

PHF3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr6:63,635,802-63,779,336

External References & Databases

Ensembl (ENSG00000118482)

Transcript & Mutation Effects

hg38 • Region Span ~143.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PHF3 variants in ClinVar

7 Conditions Cataloged

not specifiedTotal: 260

PHF3-related disorderTotal: 56

not providedTotal: 25

Neurodevelopmental disorderTotal: 1

Autism spectrum disorderTotal: 1

Neurodevelopmental delayTotal: 1

Intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370348.2. 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			2 clinvar	18 clinvar	2 clinvar	22
missense			258 clinvar	28 clinvar	9 clinvar	295
nonsense			3 clinvar			3
start loss						0
frameshift			5 clinvar			5
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	273	46	11	330

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001370348.2	RefSeq	NP_001357277.1	15	MANE Select
ENST00000262043.8	Ensembl	ENSP00000262043.4	15	MANE Select
NM_001290259.2	RefSeq	NP_001277188.1	14	Standard
NM_001290260.2	RefSeq	NP_001277189.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transcription, DNA-templated
multicellular organism development

Molecular Function

molecular_function
metal ion binding

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262043
Coding exons: 15
Length: 143505
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 34
Defined: 125746
p: 0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.755	972	1.04e+3	0.934	0.0000514	13568
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00025	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0921

Intolerance Scores

LoFtool: 0.272
RVIS EVS: -0.8
RVIS percentile EVS: 12.1

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.171

Gene Damage Prediction

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