PHF10

PHD finger protein 10, the group of PHD finger proteins|BAF complex|PBAF complex

Basic information

Region (hg38): 6:169703902-169725566

Links

ENSG00000130024 ∙ NCBI:55274 ∙ OMIM:613069 ∙ HGNC:18250 ∙ Uniprot:Q8WUB8 ∙ 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 PHF10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF10 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				1	1	2
missense			18	1		19
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	1

Variants in PHF10

This is a list of pathogenic ClinVar variants found in the PHF10 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-169704017-T-G		not specified	Uncertain significance (Jan 22, 2024)
6-169704059-C-G		not specified	Uncertain significance (Jan 03, 2024)
6-169704085-C-A		not specified	Uncertain significance (Feb 06, 2023)
6-169704085-C-T		not specified	Uncertain significance (Feb 28, 2023)
6-169705159-C-T		not specified	Uncertain significance (Apr 01, 2024)
6-169705217-G-A		not specified	Uncertain significance (Jan 22, 2024)
6-169705282-G-A		not specified	Uncertain significance (Nov 15, 2021)
6-169705620-A-G			Likely benign (Jun 01, 2022)
6-169705629-T-C			Benign (Jan 25, 2018)
6-169705642-A-G		not specified	Uncertain significance (Jun 06, 2023)
6-169705703-T-G		not specified	Likely benign (Oct 06, 2021)
6-169710265-C-T		not specified	Uncertain significance (Feb 05, 2024)
6-169710289-T-C		not specified	Uncertain significance (Dec 22, 2023)
6-169712420-C-T		not specified	Uncertain significance (May 07, 2024)
6-169714798-C-A		not specified	Uncertain significance (Feb 27, 2023)
6-169718825-T-G		not specified	Uncertain significance (Jun 11, 2024)
6-169721057-T-C		not specified	Uncertain significance (Feb 28, 2023)
6-169721071-G-A		not specified	Uncertain significance (Mar 06, 2023)
6-169721109-A-C		not specified	Uncertain significance (May 03, 2023)
6-169723861-C-T		not specified	Uncertain significance (May 27, 2022)
6-169723888-G-A		not specified	Uncertain significance (Jan 24, 2024)
6-169723889-G-C		not specified	Uncertain significance (Sep 20, 2023)
6-169723894-G-A		not specified	Uncertain significance (Mar 28, 2024)
6-169723895-G-A		not specified	Uncertain significance (Oct 13, 2023)
6-169723906-G-A		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF10	protein_coding	protein_coding	ENST00000339209	12	20151

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000288	0.999	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	173	253	0.684	0.0000129	3252
Missense in Polyphen		33	62.399	0.52886		776
Synonymous	-0.159	84	82.2	1.02	0.00000371	898
Loss of Function	3.01	11	28.3	0.389	0.00000152	359

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000279	0.000276
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000160	0.000149
Middle Eastern	0.0000545	0.0000544
South Asian	0.000132	0.000131
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in transcription activity regulation by chromatin remodeling. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and is required for the proliferation of neural progenitors. During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron- specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). {ECO:0000250}.
• Pathway: Hepatocellular carcinoma - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.284
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.258
• hipred: Y
• hipred_score: 0.683
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• 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: Phf10
• Phenotype: normal phenotype

Gene ontology

• Biological process: nervous system development;histone acetylation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: histone acetyltransferase complex;nuclear chromatin;nucleus;npBAF complex
• Molecular function: histone acetyltransferase activity;histone binding;metal ion binding