PHF11

protein-coding

PHD finger protein 11, the group of PHD finger proteins

Gene summary

This gene encodes a protein containing a PHD (plant homeodomain) type zinc finger. This gene has been identified in some studies as a candidate gene for asthma. Naturally-occurring readthrough transcription may occur from the upstream SETDB2 (SET domain bifurcated 2) gene to this locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

MANE transcript

NM_001040443.3

Inheritance

—

ClinVar variants

U:45B:3

Top phenotype

PHF11-related disorder

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr13:49,495,610-49,528,981

External References & Databases

Ensembl (ENSG00000136147)

Transcript & Mutation Effects

hg38 • Region Span ~33.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PHF11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 44

PHF11-related disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001040443.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			43 clinvar	2 clinvar		45
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	45	3	0	48

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001040443.3	RefSeq	NP_001035533.1	10	MANE Select
ENST00000378319.8	Ensembl	ENSP00000367570.3	10	MANE Select
NM_001040444.3	RefSeq	NP_001035534.1	9	Standard
NM_001419873.1	RefSeq	NP_001406802.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

metal ion binding

Cellular Component

nucleoplasm
nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378319
Coding exons: 10
Length: 33378
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 26
Defined: 125738
p: 0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.04	121	158	0.768	0.00000754	2166
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00083	0.00082	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.00014	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.111

Gene Damage Prediction

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