PHF14

PHD finger protein 14, the group of PHD finger proteins

Basic information

Region (hg38): 7:10973336-11169623

Links

ENSG00000106443 ∙ NCBI:9678 ∙ OMIM:619907 ∙ HGNC:22203 ∙ Uniprot:O94880 ∙ 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 PHF14 gene.

• not_specified (68 variants)
• not_provided (2 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF14 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001007157.2. 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				1		1
missense			67	2		69
nonsense				1		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	4	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF14	protein_coding	protein_coding	ENST00000403050	17	195752

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.265	0.735	124635	0	15	124650	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.54	277	424	0.653	0.0000206	5840
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000597	0.0000597
Ashkenazi Jewish	0.000201	0.000199
East Asian	0.00	0.00
Finnish	0.0000930	0.0000928
European (Non-Finnish)	0.0000749	0.0000708
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.506
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.78

Haploinsufficiency Scores

• pHI: 0.537
• hipred: Y
• hipred_score: 0.554
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.893

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phf14
• 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); respiratory system phenotype; skeleton phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• 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
• Cellular component: nucleus
• Molecular function: protein binding;metal ion binding