PHF23

PHD finger protein 23, the group of PHD finger proteins

Basic information

Region (hg38): 17:7235029-7239722

Links

ENSG00000040633 ∙ NCBI:79142 ∙ OMIM:612910 ∙ HGNC:28428 ∙ Uniprot:Q9BUL5 ∙ 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 PHF23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF23 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in PHF23

This is a list of pathogenic ClinVar variants found in the PHF23 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7235668-C-G		not specified	Uncertain significance (Oct 12, 2021)
17-7235720-G-T		not specified	Uncertain significance (Aug 12, 2021)
17-7236077-G-A		not specified	Uncertain significance (Nov 23, 2021)
17-7236092-G-A		not specified	Uncertain significance (Apr 25, 2022)
17-7236113-C-G		not specified	Uncertain significance (Sep 14, 2023)
17-7236140-C-T		not specified	Uncertain significance (Apr 13, 2022)
17-7236176-C-G		not specified	Uncertain significance (Mar 25, 2024)
17-7236189-G-C		not specified	Uncertain significance (Nov 22, 2022)
17-7236206-G-A		not specified	Uncertain significance (Jun 29, 2023)
17-7236239-C-A		not specified	Uncertain significance (May 31, 2023)
17-7236244-C-T		not specified	Uncertain significance (Apr 17, 2023)
17-7236245-G-A		not specified	Uncertain significance (Feb 12, 2024)
17-7236341-A-T		not specified	Uncertain significance (Dec 15, 2023)
17-7236344-C-T		not specified	Uncertain significance (Oct 27, 2022)
17-7236469-G-A		not specified	Uncertain significance (Oct 03, 2022)
17-7236550-G-T		not specified	Uncertain significance (May 25, 2022)
17-7236563-G-A		not specified	Uncertain significance (Feb 06, 2023)
17-7236574-C-T		not specified	Uncertain significance (Oct 14, 2023)
17-7236575-G-A		not specified	Uncertain significance (Feb 16, 2023)
17-7236677-G-A		not specified	Uncertain significance (Jun 27, 2022)
17-7236736-G-T		not specified	Uncertain significance (Dec 28, 2023)
17-7236737-A-T		not specified	Uncertain significance (Dec 28, 2023)
17-7237452-A-G		not specified	Uncertain significance (Mar 02, 2023)
17-7237636-T-C		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF23	protein_coding	protein_coding	ENST00000320316	5	4695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00226	124781	0	2	124783	0.00000801

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.960	193	234	0.824	0.0000135	2605
Missense in Polyphen		49	80.306	0.61016		965
Synonymous	-2.39	116	87.5	1.33	0.00000481	848
Loss of Function	3.91	0	17.8	0.00	0.00000128	178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a negative regulator of autophagy, through promoting ubiquitination and degradation of LRSAM1, an E3 ubiquitin ligase that promotes autophagy in response to starvation or infecting bacteria. {ECO:0000269|PubMed:25484098}.
• Disease: DISEASE: Note=A chromosomal aberration involving PHF23 is found in a patient with acute myeloid leukemia (AML). Translocation t(11;17)(p15;p13) with NUP98.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.334
• hipred: Y
• hipred_score: 0.594
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phf23

Gene ontology

• Biological process: autophagy;mitotic chromosome condensation;positive regulation of protein ubiquitination;negative regulation of autophagosome maturation;negative regulation of autophagosome assembly
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: chromatin binding;protein binding;metal ion binding