PHF11

Summary

PHF11 (PHD finger protein 11, HGNC:17024) is a protein-coding gene on chromosome 13q14.2, encoding PHD finger protein 11 (Q9UIL8). Positive regulator of Th1-type cytokine gene expression.

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.

Source: NCBI Gene 51131 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 55 total
• MANE Select transcript: NM_001040443

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17024
Approved symbol	PHF11
Name	PHD finger protein 11
Location	13q14.2
Locus type	gene with protein product
Status	Approved
Aliases	NY-REN-34, BCAP, IGER
Ensembl gene	ENSG00000136147
Ensembl biotype	protein_coding
OMIM	607796
Entrez	51131

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 12 protein_coding, 7 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000357596, ENST00000378319, ENST00000426879, ENST00000442195, ENST00000460489, ENST00000465045, ENST00000467763, ENST00000476953, ENST00000481509, ENST00000482487, ENST00000485919, ENST00000486276, ENST00000487433, ENST00000488605, ENST00000488958, ENST00000495157, ENST00000496612, ENST00000496623, ENST00000873989, ENST00000873990, ENST00000941732, ENST00000941733

RefSeq mRNA: 6 — MANE Select: NM_001040443 NM_001040443, NM_001040444, NM_001419873, NM_001419874, NM_001419875, NM_001419876

CCDS: CCDS31975, CCDS41887

Canonical transcript exons

ENST00000378319 — 10 exons

Exon	Start	End
ENSE00002229157	49495953	49496095
ENSE00003515172	49506635	49506756
ENSE00003525399	49528511	49528976
ENSE00003530802	49523175	49523241
ENSE00003532766	49518018	49518151
ENSE00003534685	49526387	49526458
ENSE00003557622	49520894	49520940
ENSE00003619918	49524085	49524216
ENSE00003628747	49513059	49513166
ENSE00003649398	49522043	49522107

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 97.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.5785 / max 256.1881, expressed in 1780 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
135123	28.5410	1780
207032	0.0230	7
135124	0.0145	3

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
left lobe of thyroid gland	UBERON:0001120	97.43	gold quality
right lobe of thyroid gland	UBERON:0001119	97.31	gold quality
granulocyte	CL:0000094	97.28	gold quality
thyroid gland	UBERON:0002046	97.21	gold quality
spleen	UBERON:0002106	97.11	gold quality
right adrenal gland cortex	UBERON:0035827	96.96	gold quality
metanephros cortex	UBERON:0010533	96.92	gold quality
body of pancreas	UBERON:0001150	96.82	gold quality
mucosa of stomach	UBERON:0001199	96.82	gold quality
monocyte	CL:0000576	96.80	gold quality
mononuclear cell	CL:0000842	96.79	gold quality
right adrenal gland	UBERON:0001233	96.76	gold quality
leukocyte	CL:0000738	96.71	gold quality
endocervix	UBERON:0000458	96.71	gold quality
right uterine tube	UBERON:0001302	96.65	gold quality
calcaneal tendon	UBERON:0003701	96.61	gold quality
left adrenal gland	UBERON:0001234	96.55	gold quality
left adrenal gland cortex	UBERON:0035825	96.55	gold quality
adrenal cortex	UBERON:0001235	96.54	gold quality
right coronary artery	UBERON:0001625	96.50	gold quality
lymph node	UBERON:0000029	96.40	gold quality
small intestine Peyer’s patch	UBERON:0003454	96.26	gold quality
minor salivary gland	UBERON:0001830	96.24	gold quality
ectocervix	UBERON:0012249	96.18	gold quality
body of uterus	UBERON:0009853	96.17	gold quality
skin of abdomen	UBERON:0001416	96.16	gold quality
tibial nerve	UBERON:0001323	96.11	gold quality
subcutaneous adipose tissue	UBERON:0002190	96.10	gold quality
saliva-secreting gland	UBERON:0001044	96.05	gold quality
descending thoracic aorta	UBERON:0002345	96.05	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.04

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NFKB, POU2F1, REL

Literature-anchored findings (GeneRIF, showing 10)

• Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma. (PMID:12754510)
• Results provide some further support for the role of genetic variation in PHF11 in asthma susceptibility. (PMID:17702965)
• PHF11 is a regulator of T(H)1-type cytokine gene expression (PMID:18405956)
• PHF11 is unlikely to contain polymorphic loci that have a major impact on asthma susceptibility in two independent populations. (PMID:19386584)
• rs1046295 and rs16659 associated with asthma susceptibility in a Han Chinese population (PMID:19672052)
• We were unable to confirm associations of single nucleotide polymorphisms of the positional candidates DPP10 and PHF11 with wheeze. Significant associations with reported and examined eczema were only observed for DPP10. (PMID:20085599)
• contributes to T-cell activation and viability (PMID:20421878)
• PHF11 (PHD finger protein 11) is not a major candidate gene for asthma or eczema in Chinese children (PMID:20717939)
• the single nucleotide polymorphism rs1046295 of PHF11 modulates allele-specific binding by the octamer-binding transcription factor 1 (PMID:21320718)
• data suggest that BCAP exists as two isoforms with subtly different roles in inhibition of ciliogenesis. Both are required to prevent ciliogenesis and one additionally controls cilium length after ciliogenesis has completed. (PMID:28775150)

Cross-species orthologs

11 orthologs

Organism	Symbol	Gene ID
mus_musculus	Phf11a	ENSMUSG00000044703
mus_musculus	Phf11d	ENSMUSG00000068245
mus_musculus	Phf11c	ENSMUSG00000091144
mus_musculus	Phf11b	ENSMUSG00000091649
rattus_norvegicus	Phf11	ENSRNOG00000053891
rattus_norvegicus		ENSRNOG00000078984
rattus_norvegicus		ENSRNOG00000079764
rattus_norvegicus		ENSRNOG00000084041
rattus_norvegicus		ENSRNOG00000091132
drosophila_melanogaster	pie	FBGN0005683
drosophila_melanogaster	Phf7	FBGN0031091

Paralogs (3): PHF7 (ENSG00000010318), G2E3 (ENSG00000092140), PHF6 (ENSG00000156531)

Protein

Protein identifiers

PHD finger protein 11 — Q9UIL8 (reviewed: Q9UIL8)

Alternative names: BRCA1 C-terminus-associated protein, Renal carcinoma antigen NY-REN-34

All UniProt accessions (7): B4DTX8, C9JQV2, C9JWH0, Q9UIL8, H0Y4X7, J3KR57, X6RH80

UniProt curated annotations — full annotation on UniProt →

Function. Positive regulator of Th1-type cytokine gene expression.

Subunit / interactions. Interacts with BRCA1 and RELA.

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in T and B-cells, as well as natural killer and mature dendritic cells. Expressed at higher levels in Th1 as compared to Th2 cells. Expressed at low levels in all normal tissues tested, including lung, testis, small intestine, breast, liver and placenta.

Polymorphism. Variation in PHF11 seems to be associated with propensity to childhood atopic dermatitis and asthma.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UIL8-1	1	yes
Q9UIL8-2	2

RefSeq proteins (6): NP_001035533, NP_001035534, NP_001406802, NP_001406803, NP_001406804, NP_001406805 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001965	Znf_PHD	Domain
IPR011011	Znf_FYVE_PHD	Homologous_superfamily
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR034732	EPHD	Domain
IPR051188	PHD-type_Zinc_Finger	Family

Pfam: PF13771

UniProt features (4 total): zinc finger region 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UIL8-F1	74.29	0.46

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 150 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, ONKEN_UVEAL_MELANOMA_UP, WANG_LMO4_TARGETS_DN, SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, GNF2_DDX5, GNF2_PTPRC, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, chr13q14, GOCC_NUCLEAR_ENVELOPE, GNF2_VAV1, GOCC_NUCLEAR_MEMBRANE, GNF2_CD53, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, CHEN_METABOLIC_SYNDROM_NETWORK

GO Biological Process (0):

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nuclear membrane (GO:0031965)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
nucleus	1
nuclear envelope	1
organelle membrane	1

Protein interactions and networks

STRING

1632 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PHF11	SETDB2	Q96T68	941
PHF11	ADAM33	Q9BZ11	905
PHF11	DPP10	Q8N608	818
PHF11	SPINK5	Q9NQ38	754
PHF11	NPSR1	Q6W5P4	717
PHF11	MS4A2	Q01362	663
PHF11	RCBTB1	Q8NDN9	602
PHF11	HLA-G	P17693	600
PHF11	SART1	O43290	583
PHF11	CDADC1	Q9BWV3	574
PHF11	CCL24	O00175	567
PHF11	CCL26	Q9Y258	549
PHF11	CCL11	P50877	524
PHF11	PTGDR2	Q9Y5Y4	524
PHF11	NOD1	Q9Y239	523

IntAct

27 interactions, top by confidence:

A	B	Type	Score
SDCBP	PHF11	psi-mi:“MI:0915”(physical association)	0.560
NUTF2	PHF11	psi-mi:“MI:0915”(physical association)	0.560
TEKT4	PHF11	psi-mi:“MI:0915”(physical association)	0.560
TRIM41	PHF11	psi-mi:“MI:0915”(physical association)	0.560
SPATC1L	PHF11	psi-mi:“MI:0915”(physical association)	0.560
PHF11	SULT1A2	psi-mi:“MI:0915”(physical association)	0.400
PHF11	LSM8	psi-mi:“MI:0915”(physical association)	0.370
PHF11	CSNK2B	psi-mi:“MI:0915”(physical association)	0.370
PHF11	AGPAT2	psi-mi:“MI:0915”(physical association)	0.370
PIAS4	PHF11	psi-mi:“MI:0915”(physical association)	0.370
PHF11	MCPH1	psi-mi:“MI:0915”(physical association)	0.370
PHF11	ECE1	psi-mi:“MI:0915”(physical association)	0.370
PHF11	A2ML1	psi-mi:“MI:0914”(association)	0.350
SDCBP	PHF11	psi-mi:“MI:0915”(physical association)	0.000
NUTF2	PHF11	psi-mi:“MI:0915”(physical association)	0.000
TEKT4	PHF11	psi-mi:“MI:0915”(physical association)	0.000
TRIM41	PHF11	psi-mi:“MI:0915”(physical association)	0.000
SPATC1L	PHF11	psi-mi:“MI:0915”(physical association)	0.000
PHF11		psi-mi:“MI:0915”(physical association)	0.000
PHF11	fla FIII	psi-mi:“MI:0915”(physical association)	0.000
	PHF11	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (150): SULT1A2 (Affinity Capture-MS), SULT1A2 (Affinity Capture-MS), PHF11 (Two-hybrid), PHF11 (Two-hybrid), SDCBP (Two-hybrid), TRIM41 (Two-hybrid), SPATC1L (Two-hybrid), TEKT4 (Two-hybrid), SULT1A2 (Affinity Capture-MS), CBR1 (Affinity Capture-MS), GLUL (Affinity Capture-MS), S100A7 (Affinity Capture-MS), ORM1 (Affinity Capture-MS), AHSG (Affinity Capture-MS), HIST1H1B (Affinity Capture-MS)

ESM2 similar proteins: A2BGP7, A2CJ06, A6H5X4, A7E316, E2RSS3, F7BHS0, O35144, O55036, P0DOV1, Q13342, Q1LX29, Q2HJ93, Q3B7D9, Q3TD16, Q3U827, Q5I0E2, Q5I0J8, Q5NBU8, Q5RCZ8, Q5XFX8, Q60953, Q66JT0, Q6AXZ2, Q6AZF8, Q6IE82, Q6IRU7, Q6ZQF7, Q6ZV50, Q7TNY7, Q80VH0, Q8BP86, Q8BVK9, Q8BVM9, Q8C0G2, Q8C0V1, Q8C267, Q8CGE8, Q8K2H3, Q8NDB2, Q91YK2

Diamond homologs: A6H5X4, F4I443, O08550, O14686, P55200, Q03164, Q08DR0, Q2HJ93, Q4R9C4, Q5F4A1, Q5I0E2, Q5I0J8, Q5R5Z2, Q5RJY2, Q6PDK2, Q7L622, Q8BRH4, Q8BVM9, Q8IWS0, Q8NEZ4, Q9D4J7, Q9UIL8, Q9UMN6, Q61818, Q6AXW4, Q7Z5J4, Q9BWX1, Q9DAG9, Q24742, Q9EPQ8, Q9UGU0, Q9VKW2, P20659

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

55 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	37
Likely benign	4
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1777 predictions. Top by Δscore:

Variant	Effect	Δscore
13:49496074:G:GT	donor_gain	1.0000
13:49513050:A:AG	acceptor_gain	1.0000
13:49518142:G:GT	donor_gain	1.0000
13:49518148:A:AG	donor_gain	1.0000
13:49518148:A:G	donor_gain	1.0000
13:49518152:G:GG	donor_gain	1.0000
13:49523249:C:G	donor_gain	1.0000
13:49524083:A:AG	acceptor_gain	1.0000
13:49524084:G:GG	acceptor_gain	1.0000
13:49496097:T:A	donor_loss	0.9900
13:49513051:A:G	acceptor_gain	0.9900
13:49513058:GCT:G	acceptor_gain	0.9900
13:49513058:GCTGT:G	acceptor_gain	0.9900
13:49513163:GTTG:G	donor_gain	0.9900
13:49513167:GT:G	donor_loss	0.9900
13:49513168:TAAGT:T	donor_loss	0.9900
13:49513169:A:AG	donor_loss	0.9900
13:49518132:G:GT	donor_gain	0.9900
13:49518143:A:T	donor_gain	0.9900
13:49520938:GTG:G	donor_gain	0.9900
13:49522042:GCT:G	acceptor_gain	0.9900
13:49522042:GCTA:G	acceptor_gain	0.9900
13:49522042:GCTAA:G	acceptor_gain	0.9900
13:49524079:TCTTA:T	acceptor_loss	0.9900
13:49524080:CTTAG:C	acceptor_loss	0.9900
13:49524081:TTA:T	acceptor_loss	0.9900
13:49524082:TA:T	acceptor_loss	0.9900
13:49524084:GAT:G	acceptor_gain	0.9900
13:49524212:ATCAG:A	donor_loss	0.9900
13:49524213:TCAG:T	donor_loss	0.9900

AlphaMissense

2179 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:49513119:T:C	F93L	0.998
13:49513121:T:A	F93L	0.998
13:49513121:T:G	F93L	0.998
13:49518057:T:A	C122S	0.997
13:49518058:G:C	C122S	0.997
13:49518089:C:A	H132Q	0.997
13:49518089:C:G	H132Q	0.997
13:49506751:T:C	C71R	0.996
13:49513154:A:C	R104S	0.996
13:49513154:A:T	R104S	0.996
13:49518021:T:C	C110R	0.996
13:49506740:C:A	A67D	0.995
13:49506744:T:A	H68Q	0.995
13:49506744:T:G	H68Q	0.995
13:49506753:T:G	C71W	0.995
13:49513120:T:C	F93S	0.995
13:49518021:T:A	C110S	0.995
13:49518022:G:C	C110S	0.995
13:49518057:T:C	C122R	0.995
13:49518100:C:A	A136D	0.995
13:49506673:T:C	C45R	0.994
13:49518030:T:A	C113S	0.994
13:49518030:T:C	C113R	0.994
13:49518031:G:C	C113S	0.994
13:49518096:T:C	C135R	0.994
13:49506673:T:A	C45S	0.993
13:49506674:G:C	C45S	0.993
13:49506682:T:C	C48R	0.993
13:49506751:T:A	C71S	0.993
13:49506752:G:C	C71S	0.993

dbSNP variants (sampled 300 via entrez): RS1000155730 (13:49507288 T>C), RS1000438651 (13:49507114 C>G), RS1000469548 (13:49505985 TTTC>T), RS1000474463 (13:49526804 A>T), RS1000659871 (13:49494553 T>G), RS1000778904 (13:49494023 A>C,G), RS1000890524 (13:49512739 C>T), RS1000898588 (13:49519026 G>A,T), RS1000925706 (13:49512428 C>T), RS1001075734 (13:49525456 C>T), RS1001087655 (13:49518924 C>G,T), RS1001442366 (13:49526216 C>G), RS1001680383 (13:49519858 G>A), RS1001701017 (13:49513393 C>T), RS1001775247 (13:49523795 T>A)

Disease associations

OMIM: gene MIM:607796 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST000960_11	Cardiac hypertrophy	5.000000e-06
GCST002715_4	Breastfeeding duration	2.000000e-06
GCST007052_3	Lipoprotein (a) levels	2.000000e-06
GCST010002_186	Refractive error	1.000000e-36

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0002503	cardiac hypertrophy
EFO:0006864	breastfeeding duration
EFO:0006925	lipoprotein A measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

49 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	6
trichostatin A	increases expression, affects cotreatment	3
potassium chromate(VI)	affects cotreatment, decreases expression	2
Vorinostat	decreases expression	2
Acetaminophen	increases expression, decreases expression	2
Air Pollutants	increases oxidation, increases expression, affects cotreatment, decreases expression, increases abundance	2
Nickel	increases expression	2
Tretinoin	increases expression	2
Particulate Matter	increases abundance, increases expression, affects response to substance	2
bisphenol F	affects cotreatment, increases expression	1
TAK-243	increases sumoylation	1
alpha-pinene	affects cotreatment, decreases expression, increases oxidation, increases abundance	1
bisphenol A	decreases expression	1
beta-lapachone	increases expression	1
sodium arsenite	decreases expression	1
methacrylaldehyde	affects cotreatment, decreases expression, increases oxidation, increases abundance	1
epigallocatechin gallate	decreases expression, affects cotreatment	1
chromium hexavalent ion	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
dorsomorphin	increases expression, affects cotreatment	1
NSC 689534	affects binding, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Decitabine	decreases expression, decreases reaction	1
Sunitinib	decreases expression	1
Acrolein	affects cotreatment, decreases expression, increases oxidation, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Copper	affects binding, increases expression	1
Demecolcine	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.