PHF24

PHD finger protein 24, the group of PHD finger proteins

Basic information

Region (hg38): 9:34957608-34982544

Previous symbols: [ "KIAA1045" ]

Links

ENSG00000122733 ∙ NCBI:23349 ∙ OMIM:619928 ∙ HGNC:29180 ∙ Uniprot:Q9UPV7 ∙ 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 PHF24 gene.

• not_specified (55 variants)
• Breast_ductal_adenocarcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF24 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015297.3. 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						0
missense			55	1		56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF24	protein_coding	protein_coding	ENST00000242315	7	25058

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0700	0.929	124789	0	13	124802	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.721	231	264	0.875	0.0000174	2609
Missense in Polyphen		75	104.69	0.71643		1082
Synonymous	0.193	95	97.4	0.975	0.00000564	808
Loss of Function	3.05	6	21.1	0.284	0.00000137	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000588	0.0000588
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.0000710	0.0000706
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000335	0.000330

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• pHI: 0.199
• hipred: Y
• hipred_score: 0.696
• ghis: 0.560

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Phf24
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: gamma-aminobutyric acid signaling pathway;regulation of G protein-coupled receptor signaling pathway;regulation of synaptic transmission, GABAergic;detection of mechanical stimulus involved in sensory perception of pain
• Molecular function: metal ion binding