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.

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.

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						0
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in PHF24

This is a list of pathogenic ClinVar variants found in the PHF24 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-34971320-C-T		not specified	Uncertain significance (Mar 23, 2023)
9-34971375-A-T		not specified	Uncertain significance (Sep 16, 2021)
9-34971402-G-A		not specified	Uncertain significance (Aug 02, 2022)
9-34971423-G-C		not specified	Uncertain significance (May 29, 2024)
9-34971428-C-T		not specified	Uncertain significance (Jan 10, 2023)
9-34971431-C-T		not specified	Uncertain significance (Dec 19, 2023)
9-34971432-G-A		not specified	Uncertain significance (Feb 11, 2022)
9-34971435-G-T		not specified	Uncertain significance (Oct 26, 2022)
9-34971521-G-A		not specified	Uncertain significance (Jun 17, 2022)
9-34971524-C-T		not specified	Uncertain significance (Oct 05, 2023)
9-34971540-G-A		Breast ductal adenocarcinoma	Uncertain significance (Jul 20, 2015)
9-34971581-A-G		not specified	Uncertain significance (Aug 02, 2021)
9-34971602-C-T		not specified	Uncertain significance (Mar 15, 2024)
9-34971624-G-A		not specified	Uncertain significance (Apr 07, 2022)
9-34971657-G-T		not specified	Uncertain significance (Feb 28, 2023)
9-34972367-G-A		not specified	Uncertain significance (Jan 26, 2022)
9-34972446-G-A		not specified	Uncertain significance (Mar 25, 2024)
9-34972449-G-A		not specified	Uncertain significance (Feb 13, 2023)
9-34972479-C-T		not specified	Uncertain significance (Jan 26, 2022)
9-34976212-C-T		not specified	Uncertain significance (Apr 09, 2024)
9-34976571-G-A		not specified	Uncertain significance (Jan 26, 2022)
9-34976733-G-A		not specified	Uncertain significance (Jan 19, 2022)
9-34977086-T-C		not specified	Uncertain significance (Dec 06, 2022)
9-34977134-G-A		not specified	Likely benign (Aug 15, 2023)
9-34977135-C-T		not specified	Uncertain significance (Oct 05, 2023)

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