PHF14

protein-coding

PHD finger protein 14, the group of PHD finger proteins

Gene summary

Enables histone binding activity. Predicted to be involved in several processes, including germinal center B cell differentiation; negative regulation of mesenchymal cell proliferation involved in lung development; and negative regulation of platelet-derived growth factor receptor-alpha signaling pathway. Located in chromatin; cytoplasm; and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001007157.2

Inheritance

—

ClinVar variants

U:95B:4

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr7:10,973,336-11,169,623

External References & Databases

Ensembl (ENSG00000106443)

Transcript & Mutation Effects

hg38 • Region Span ~196.3 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 PHF14 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 81

not providedTotal: 3

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001007157.2. 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			3 clinvar	1 clinvar		4
missense			85 clinvar	2 clinvar		87
nonsense			3 clinvar	1 clinvar		4
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	95	4	0	99

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001007157.2	RefSeq	NP_001007158.1	18	MANE Select
ENST00000634607.2	Ensembl	ENSP00000489535.1	18	MANE Select
NM_014660.4	RefSeq	NP_055475.2	17	Standard
ENST00000403050.7	Ensembl	ENSP00000385795.3	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
lung alveolus development
negative regulation of platelet-derived growth factor receptor-alpha signaling pathway
negative regulation of mesenchymal cell proliferation involved in lung development

Molecular Function

protein binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000403050
Coding exons: 17
Length: 195752
Individuals with no LoFs: 124635
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 124650
p: 0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.54	277	424	0.653	0.0000206	5840
Missense (PolyPhen)		50	137.78	0.36289		1792
Synonymous	-0.253	146	142	1.03	0.00000688	1557
Loss of Function	4.66	10	42.9	0.233	0.00000237	596

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000060	0.000058	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0	0.0	absent
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.000075	0.000071	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.506
RVIS EVS: -0.53
RVIS percentile EVS: 20.78

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.893

Gene Damage Prediction

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