PHF11

PHD finger protein 11, the group of PHD finger proteins

Basic information

Region (hg38): 13:49495609-49528981

Links

ENSG00000136147 ∙ NCBI:51131 ∙ OMIM:607796 ∙ HGNC:17024 ∙ Uniprot:Q9UIL8 ∙ 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 PHF11 gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF11 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			12	1		13
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	13	1	0

Variants in PHF11

This is a list of pathogenic ClinVar variants found in the PHF11 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-49496108-GGGGC-G			Benign (Jan 17, 2024)
13-49506658-A-G		not specified	Uncertain significance (Mar 06, 2023)
13-49506663-A-T		not specified	Uncertain significance (Oct 04, 2022)
13-49506711-A-G		PHF11-related disorder	Benign (Oct 17, 2019)
13-49506734-T-C		not specified	Uncertain significance (Nov 09, 2023)
13-49506740-C-T		not specified	Uncertain significance (Dec 20, 2023)
13-49513096-A-T		not specified	Uncertain significance (Feb 15, 2023)
13-49513117-G-A		not specified	Likely benign (Nov 05, 2021)
13-49513139-G-T		not specified	Uncertain significance (May 23, 2023)
13-49518113-C-T		PHF11-related disorder	Likely benign (Jun 20, 2019)
13-49520866-T-TACAATTCTTTGAAATTAAATATTTC		PHF11-related disorder	Likely benign (Aug 13, 2019)
13-49520935-A-C		not specified	Uncertain significance (Sep 17, 2021)
13-49522084-C-A		not specified	Uncertain significance (Aug 17, 2022)
13-49522084-C-T		not specified	Uncertain significance (Jun 11, 2021)
13-49523181-G-A		not specified	Uncertain significance (Feb 09, 2023)
13-49524098-A-C		not specified	Uncertain significance (Nov 15, 2023)
13-49524141-T-A		not specified	Uncertain significance (Feb 10, 2022)
13-49526401-G-A		not specified	Uncertain significance (Nov 07, 2022)
13-49526431-G-A		not specified	Uncertain significance (Jul 30, 2023)
13-49528603-T-C		not specified	Uncertain significance (Jun 01, 2022)
13-49528642-T-A		not specified	Uncertain significance (Jan 06, 2023)
13-49528674-G-A		PHF11-related disorder	Benign (Oct 17, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF11	protein_coding	protein_coding	ENST00000378319	10	33378

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.35e-8	0.376	125712	0	26	125738	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	121	158	0.768	0.00000754	2166
Missense in Polyphen		24	37.795	0.635		536
Synonymous	0.679	50	56.5	0.885	0.00000307	578
Loss of Function	0.730	13	16.2	0.804	7.47e-7	230

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000830	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000352
Middle Eastern	0.000830	0.000816
South Asian	0.000136	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positive regulator of Th1-type cytokine gene expression. {ECO:0000269|PubMed:18405956}.

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.738
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.0989
• hipred: N
• hipred_score: 0.123
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.111

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phf11d
• Phenotype: immune system phenotype

Gene ontology

• Cellular component: nucleoplasm;nuclear membrane
• Molecular function: metal ion binding