ZNF248

Summary

ZNF248 (zinc finger protein 248, HGNC:13041) is a protein-coding gene on chromosome 10p11.21, encoding Zinc finger protein 248 (Q8NDW4). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 57209 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 69 total
• MANE Select transcript: NM_021045

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13041
Approved symbol	ZNF248
Name	zinc finger protein 248
Location	10p11.21
Locus type	gene with protein product
Status	Approved
Aliases	bA162G10.3
Ensembl gene	ENSG00000198105
Ensembl biotype	protein_coding
OMIM	621128
Entrez	57209

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 24 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000357328, ENST00000374648, ENST00000395867, ENST00000395873, ENST00000395874, ENST00000485560, ENST00000494133, ENST00000611278, ENST00000615949, ENST00000854418, ENST00000854419, ENST00000854420, ENST00000854421, ENST00000854422, ENST00000854423, ENST00000854424, ENST00000854425, ENST00000854426, ENST00000854427, ENST00000854428, ENST00000854429, ENST00000914960, ENST00000914961, ENST00000945390, ENST00000945391, ENST00000945392

RefSeq mRNA: 30 — MANE Select: NM_021045 NM_001267597, NM_001267605, NM_001267606, NM_001267607, NM_001352469, NM_001352470, NM_001352471, NM_001352472, NM_001352473, NM_001352474, NM_001352476, NM_001352477, NM_001352478, NM_001352479, NM_001352480, NM_001352481, NM_001352482, NM_001352483, NM_001352484, NM_001352485, NM_001352486, NM_001352487, NM_001352488, NM_001352489, NM_001352490, NM_001352491, NM_001352492, NM_001352493, NM_001352494, NM_021045

CCDS: CCDS58077, CCDS7194, CCDS73087, CCDS86083

Canonical transcript exons

ENST00000395867 — 6 exons

Exon	Start	End
ENSE00001369757	37856435	37856532
ENSE00001843405	37857185	37857610
ENSE00003561317	37856296	37856337
ENSE00003802807	37837617	37837712
ENSE00003808556	37837985	37838111
ENSE00003915909	37828763	37833116

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 95.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.0431 / max 126.6881, expressed in 1357 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
109124	2.0090	917
109125	1.7086	934
109123	0.3113	136
109122	0.0142	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
middle temporal gyrus	UBERON:0002771	95.50	gold quality
Brodmann (1909) area 23	UBERON:0013554	92.82	gold quality
paraflocculus	UBERON:0005351	92.56	gold quality
cerebellar hemisphere	UBERON:0002245	90.86	gold quality
cerebellar cortex	UBERON:0002129	90.82	gold quality
cerebellum	UBERON:0002037	90.67	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.56	gold quality
cortical plate	UBERON:0005343	89.49	gold quality
primary visual cortex	UBERON:0002436	89.21	gold quality
tibia	UBERON:0000979	89.04	gold quality
cerebellar vermis	UBERON:0004720	88.61	gold quality
frontal pole	UBERON:0002795	88.10	gold quality
tendon of biceps brachii	UBERON:0008188	87.91	gold quality
calcaneal tendon	UBERON:0003701	87.52	gold quality
pituitary gland	UBERON:0000007	87.18	gold quality
middle frontal gyrus	UBERON:0002702	87.14	gold quality
occipital lobe	UBERON:0002021	86.89	gold quality
muscle layer of sigmoid colon	UBERON:0035805	86.81	gold quality
ganglionic eminence	UBERON:0004023	86.66	gold quality
tendon	UBERON:0000043	86.53	gold quality
adenohypophysis	UBERON:0002196	86.16	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.54	gold quality
right uterine tube	UBERON:0001302	85.42	gold quality
lateral nuclear group of thalamus	UBERON:0002736	85.35	gold quality
body of uterus	UBERON:0009853	85.25	gold quality
ovary	UBERON:0000992	85.09	gold quality
right frontal lobe	UBERON:0002810	84.89	gold quality
left ovary	UBERON:0002119	84.85	gold quality
Brodmann (1909) area 9	UBERON:0013540	84.54	gold quality
endocervix	UBERON:0000458	84.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.68

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

102 targeting ZNF248, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4756-5P	99.84	64.98	1809

Literature-anchored findings (GeneRIF, showing 1)

• Smoking and obesity are risk factors for LOA. ZNF248 confers increased susceptibility to LOA in African Americans. (PMID:27238579)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp248	ENSMUSG00000030145
rattus_norvegicus	Zfp248	ENSRNOG00000037251
drosophila_melanogaster	CG2712	FBGN0024975
drosophila_melanogaster	Phs	FBGN0036522
drosophila_melanogaster	CG3281	FBGN0260741

Paralogs (62): ZNF582 (ENSG00000018869), ZNF264 (ENSG00000083844), ZNF343 (ENSG00000088876), ZNF684 (ENSG00000117010), ZNF133 (ENSG00000125846), ZNF557 (ENSG00000130544), ZNF337 (ENSG00000130684), ZNF20 (ENSG00000132010), ZFP37 (ENSG00000136866), ZNF614 (ENSG00000142556), KRBOX4 (ENSG00000147121), ZNF599 (ENSG00000153896), ZNF19 (ENSG00000157429), ZNF589 (ENSG00000164048), PRDM9 (ENSG00000164256), ZNF180 (ENSG00000167384), ZNF558 (ENSG00000167785), ZNF35 (ENSG00000169981), ZNF778 (ENSG00000170100), ZNF439 (ENSG00000171291), ZNF440 (ENSG00000171295), ZNF556 (ENSG00000172000), ZNF554 (ENSG00000172006), ZNF596 (ENSG00000172748), ZNF80 (ENSG00000174255), ZNF266 (ENSG00000174652), ZNF25 (ENSG00000175395), ZNF77 (ENSG00000175691), ZNF169 (ENSG00000175787), ZNF404 (ENSG00000176222), ZNF491 (ENSG00000177599), ZNF620 (ENSG00000177842), ZNF619 (ENSG00000177873), ZNF875 (ENSG00000181666), ZNF329 (ENSG00000181894), ZFP90 (ENSG00000184939), ZNF566 (ENSG00000186017), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300)

Protein

Protein identifiers

Zinc finger protein 248 — Q8NDW4 (reviewed: Q8NDW4)

All UniProt accessions (6): Q8NDW4, A0A087WTK3, A2RUI7, B1AL40, B1AL42, S4R340

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NDW4-1	1	yes
Q8NDW4-2	2

RefSeq proteins (30): NP_001254526, NP_001254534, NP_001254535, NP_001254536, NP_001339398, NP_001339399, NP_001339400, NP_001339401, NP_001339402, NP_001339403, NP_001339405, NP_001339406, NP_001339407, NP_001339408, NP_001339409, NP_001339410, NP_001339411, NP_001339412, NP_001339413, NP_001339414, NP_001339415, NP_001339416, NP_001339417, NP_001339418, NP_001339419, NP_001339420, NP_001339421, NP_001339422, NP_001339423, NP_066383* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF01352

UniProt features (13 total): zinc finger region 8, chain 1, domain 1, cross-link 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NDW4-F1	55.52	0.22

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 341

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 79 (showing top): TGCGCANK_UNKNOWN, NAGASHIMA_NRG1_SIGNALING_DN, WGTTNNNNNAAA_UNKNOWN, GEORGES_TARGETS_OF_MIR192_AND_MIR215, chr10p11, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP, MODULE_212, VERHAAK_GLIOBLASTOMA_PRONEURAL, VANOEVELEN_MYOGENESIS_SIN3A_TARGETS, SMIRNOV_RESPONSE_TO_IR_2HR_DN, DCA_UP.V1_DN, NRF1_Q6, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY

GO Biological Process (4): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355), regulation of macromolecule metabolic process (GO:0060255), regulation of primary metabolic process (GO:0080090)

GO Molecular Function (7): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872), sequence-specific double-stranded DNA binding (GO:1990837)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of metabolic process	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
macromolecule metabolic process	1
primary metabolic process	1
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

692 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF248	TRIM4	Q9C037	449
ZNF248	CCDC74A	Q96AQ1	445
ZNF248	ZDHHC24	Q6UX98	437
ZNF248	SEPTIN8	Q92599	429
ZNF248	EXD1	Q8NHP7	424
ZNF248	SLC25A1	P53007	412
ZNF248	EXOC2	Q96KP1	412
ZNF248	PCYOX1L	Q8NBM8	410
ZNF248	CATSPERB	Q9H7T0	400
ZNF248	GXYLT1	Q4G148	398
ZNF248	PGAP2	Q9UHJ9	394
ZNF248	ZNF462	Q96JM2	387
ZNF248	H2AJ	Q9BTM1	387
ZNF248	STON2	Q8WXE9	383
ZNF248	STARD9	Q9P2P6	376

IntAct

7 interactions, top by confidence:

A	B	Type	Score
MEOX2	ZNF248	psi-mi:“MI:0915”(physical association)	0.560
ZNF248	PDCD5	psi-mi:“MI:0914”(association)	0.350
ZNF248	SYN3	psi-mi:“MI:0914”(association)	0.350
TNIK	ZNF248	psi-mi:“MI:0915”(physical association)	0.000
ZNF248	MEOX2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (13): ZNF248 (Affinity Capture-RNA), ZNF248 (Affinity Capture-RNA), ZNF248 (Two-hybrid), LRP4 (Affinity Capture-MS), DPYSL3 (Affinity Capture-MS), TRIM39 (Affinity Capture-MS), SYN3 (Affinity Capture-MS), ARIH1 (Affinity Capture-MS), ZNF432 (Affinity Capture-MS), TRIM28 (Affinity Capture-MS), ZNF248 (Affinity Capture-MS), DLD (Cross-Linking-MS (XL-MS)), ZNF248 (Affinity Capture-RNA)

ESM2 similar proteins: A0JPL0, A6NK53, E7ETH6, E9Q8G5, O14628, P21506, P51508, Q09FC8, Q13360, Q2M218, Q2M3X9, Q2VY69, Q3KQV3, Q3SY52, Q4R882, Q5HY98, Q5REN4, Q5RES8, Q68DI1, Q6NX49, Q6P280, Q6PG37, Q6V9R5, Q6ZMW2, Q7Z340, Q86XU0, Q8IYI8, Q8N587, Q8N720, Q8N859, Q8NB42, Q8NDW4, Q8NEK5, Q8WXB4, Q96MR9, Q96MU6, Q96NG8, Q96NJ3, Q96SR6, Q9BR84

Diamond homologs: A0A1W2PQL4, A0JNB1, A0JPL0, A6NK53, A6QLU5, A6QPT6, A7MBI1, A8MT65, A8MUV8, A8MWA4, B2RXC5, B4DU55, B4DX44, E9PYI1, O14628, O75346, P0CH99, P0CI00, P17014, P17030, P17032, P17098, P51786, P85977, Q02386, Q06730, Q06732, Q0VAW7, Q12901, Q13360, Q14586, Q14588, Q14590, Q16587, Q2M3X9, Q2VY69, Q32M78, Q3ZCX4, Q49AA0, Q4R6J4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

963 predictions. Top by Δscore:

Variant	Effect	Δscore
10:37837709:TACC:T	acceptor_gain	1.0000
10:37837984:CCTA:C	donor_gain	1.0000
10:37837987:A:AC	donor_gain	1.0000
10:37837988:C:CC	donor_gain	1.0000
10:37833117:C:CC	acceptor_gain	0.9900
10:37837612:CTCA:C	donor_loss	0.9900
10:37837614:CA:C	donor_loss	0.9900
10:37837711:CC:C	acceptor_gain	0.9900
10:37837712:CC:C	acceptor_gain	0.9900
10:37837713:C:CC	acceptor_gain	0.9900
10:37837979:CCTTA:C	donor_loss	0.9900
10:37837980:CTTAC:C	donor_loss	0.9900
10:37837981:TTACC:T	donor_loss	0.9900
10:37837982:TAC:T	donor_loss	0.9900
10:37837983:A:AG	donor_loss	0.9900
10:37837984:C:CT	donor_loss	0.9900
10:37838547:A:AC	donor_gain	0.9900
10:37833113:CTTT:C	acceptor_gain	0.9800
10:37837708:ATACC:A	acceptor_gain	0.9800
10:37838598:G:A	donor_gain	0.9800
10:37857545:C:CA	donor_gain	0.9800
10:37833115:TT:T	acceptor_gain	0.9700
10:37833116:TC:T	acceptor_loss	0.9700
10:37833118:T:C	acceptor_loss	0.9700
10:37834965:A:AC	donor_gain	0.9700
10:37834966:C:CC	donor_gain	0.9700
10:37837710:ACCC:A	acceptor_loss	0.9700
10:37837711:CCCT:C	acceptor_loss	0.9700
10:37837712:CCTG:C	acceptor_loss	0.9700
10:37837713:C:CG	acceptor_loss	0.9700

AlphaMissense

3884 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:37831768:G:C	F529L	0.999
10:37831768:G:T	F529L	0.999
10:37831770:A:G	F529L	0.999
10:37831835:A:G	L507P	0.999
10:37831852:G:C	F501L	0.999
10:37831852:G:T	F501L	0.999
10:37831854:A:G	F501L	0.999
10:37832020:G:C	F445L	0.999
10:37832020:G:T	F445L	0.999
10:37832022:A:G	F445L	0.999
10:37832104:A:C	F417L	0.999
10:37832104:A:T	F417L	0.999
10:37832106:A:G	F417L	0.999
10:37831684:A:C	F557L	0.998
10:37831684:A:T	F557L	0.998
10:37831686:A:G	F557L	0.998
10:37831823:T:G	Q511P	0.998
10:37831827:G:C	H510D	0.998
10:37831936:G:C	F473L	0.998
10:37831936:G:T	F473L	0.998
10:37831938:A:G	F473L	0.998
10:37831993:A:C	H454Q	0.998
10:37831993:A:T	H454Q	0.998
10:37832003:A:G	L451P	0.998
10:37831741:A:C	H538Q	0.997
10:37831741:A:T	H538Q	0.997
10:37831751:A:G	L535P	0.997
10:37831825:A:C	H510Q	0.997
10:37831825:A:T	H510Q	0.997
10:37831879:A:C	F492L	0.997

dbSNP variants (sampled 300 via entrez): RS1000028588 (10:37828675 C>A), RS1000044757 (10:37850070 C>G), RS1000077409 (10:37849753 C>A,T), RS1000087307 (10:37780713 A>C,G,T), RS1000116344 (10:37793157 C>A,T), RS1000130818 (10:37825784 C>G), RS1000160619 (10:37825641 A>G), RS1000226652 (10:37776432 T>C), RS1000315296 (10:37775704 A>T), RS1000326198 (10:37764676 G>A), RS1000347883 (10:37799420 G>A,C), RS1000364807 (10:37841651 A>G), RS1000391873 (10:37815687 A>T), RS1000438539 (10:37842049 CT>C), RS1000506142 (10:37853537 C>G)

Disease associations

OMIM: gene MIM:621128 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST000426_12	Obesity (extreme)	9.000000e-07
GCST005288_2	Extrinsic epigenetic age acceleration	7.000000e-11
GCST005288_3	Extrinsic epigenetic age acceleration	1.000000e-13
GCST009391_1214	Metabolite levels	9.000000e-07
GCST009391_126	Metabolite levels	6.000000e-07
GCST009391_1877	Metabolite levels	1.000000e-06

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0000473	epigenetic status
EFO:0022597	aging
EFO:0010420	triacylglycerol 54:2 measurement
EFO:0010355	diacylglycerol 36:2 measurement
EFO:0010414	triacylglycerol 52:2 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	decreases expression	2
Tetrachlorodibenzodioxin	decreases expression	2
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases expression	1
geraniol	decreases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
beta-methylcholine	affects expression	1
pentanal	decreases expression	1
abrine	decreases expression	1
bisphenol S	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, increases expression	1
Leflunomide	decreases expression	1
Arsenic	affects methylation	1
Cisplatin	increases expression, affects cotreatment	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	increases expression, affects cotreatment	1
Quercetin	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	decreases methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	decreases expression	1
Antirheumatic Agents	increases expression	1
Okadaic Acid	decreases expression	1
Lactic Acid	decreases expression	1
Acrylamide	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_XW24	HEK293 eGFP-ZNF248	Transformed cell line	Female

Clinical trials (associated diseases)

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