ZSCAN31

gene
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Summary

ZSCAN31 (zinc finger and SCAN domain containing 31, HGNC:14097) is a protein-coding gene on chromosome 6p22.1, encoding Zinc finger and SCAN domain-containing protein 31 (Q96LW9). May function as a transcription factor.

This gene encodes a protein containing multiple C2H2-type zinc finger motifs. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 64288 — RefSeq curated summary.

At a glance

  • GWAS associations: 30
  • Clinical variants (ClinVar): 42 total
  • MANE Select transcript: NM_030899

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14097
Approved symbolZSCAN31
Namezinc finger and SCAN domain containing 31
Location6p22.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000235109
Ensembl biotypeprotein_coding
OMIM610794
Entrez64288

Gene structure

Transcript identifiers

Ensembl transcripts: 42 — 40 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000344279, ENST00000396838, ENST00000414429, ENST00000414431, ENST00000426434, ENST00000426756, ENST00000434036, ENST00000435857, ENST00000439158, ENST00000439628, ENST00000439636, ENST00000444081, ENST00000446222, ENST00000446474, ENST00000447021, ENST00000453745, ENST00000476001, ENST00000481934, ENST00000611469, ENST00000881652, ENST00000881653, ENST00000881654, ENST00000881655, ENST00000881656, ENST00000881657, ENST00000881658, ENST00000881659, ENST00000917875, ENST00000917876, ENST00000962705, ENST00000962706, ENST00000962707, ENST00000962708, ENST00000962709, ENST00000962710, ENST00000962711, ENST00000962712, ENST00000962713, ENST00000962714, ENST00000962715, ENST00000962716, ENST00000962717

RefSeq mRNA: 8 — MANE Select: NM_030899 NM_001135215, NM_001135216, NM_001243241, NM_001243242, NM_001243243, NM_001243244, NM_030899, NM_145909

CCDS: CCDS4649, CCDS59001

Canonical transcript exons

ENST00000344279 — 4 exons

ExonStartEnd
ENSE000017155132832930328329778
ENSE000018136412833608228336148
ENSE000019758942832473728326854
ENSE000036608352832738328327533

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 89.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.3296 / max 96.0797, expressed in 1044 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
724060.9797607
724110.9300366
724100.7969308
724090.189398
724070.182569
724120.119451
724080.099242
724130.032612

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453389.03gold quality
right testisUBERON:000453489.02gold quality
testisUBERON:000047386.90gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.79gold quality
gall bladderUBERON:000211086.44gold quality
left ovaryUBERON:000211984.02gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.66gold quality
C1 segment of cervical spinal cordUBERON:000646983.39gold quality
right lobe of thyroid glandUBERON:000111983.14gold quality
muscle layer of sigmoid colonUBERON:003580582.82gold quality
ovaryUBERON:000099282.76gold quality
islet of LangerhansUBERON:000000682.72gold quality
left lobe of thyroid glandUBERON:000112082.43gold quality
lower esophagus muscularis layerUBERON:003583382.37gold quality
lower esophagusUBERON:001347382.36gold quality
gingivaUBERON:000182882.07gold quality
hindlimb stylopod muscleUBERON:000425282.06gold quality
right ovaryUBERON:000211881.88gold quality
thyroid glandUBERON:000204681.60gold quality
esophagusUBERON:000104381.30gold quality
body of uterusUBERON:000985381.27gold quality
body of stomachUBERON:000116181.26gold quality
gingival epitheliumUBERON:000194981.17gold quality
cerebellar cortexUBERON:000212981.06gold quality
cerebellar hemisphereUBERON:000224581.04gold quality
esophagogastric junction muscularis propriaUBERON:003584180.94gold quality
body of pancreasUBERON:000115080.77gold quality
esophagus mucosaUBERON:000246980.74gold quality
right hemisphere of cerebellumUBERON:001489080.58gold quality
pancreasUBERON:000126480.44gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.17

Regulation

Is transcription factor: yes

JASPAR motifs

MotifNameFamily
MA1722.1ZSCAN31More than 3 adjacent zinc fingers
MA1722.2ZSCAN31More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:27852650

miRNA regulators (miRDB)

72 targeting ZSCAN31, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3924100.0072.092394
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-453199.9969.703181
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-590-3P99.9674.346478
HSA-MIR-971899.9468.91918
HSA-MIR-497-5P99.9271.832674
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-627-3P99.9071.423316
HSA-MIR-424-5P99.8971.902641
HSA-MIR-6838-5P99.8971.942690
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-449599.8272.083080
HSA-MIR-44899.7972.372103
HSA-MIR-3150A-3P99.7664.441640
HSA-MIR-6763-5P99.7664.681767
HSA-MIR-432099.7565.80793
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-580-3P99.6769.231841
HSA-MIR-317599.6566.302031
HSA-MIR-570099.6469.882280
HSA-MIR-432899.5771.064094
HSA-MIR-4524A-5P99.5771.731193

Literature-anchored findings (GeneRIF, showing 4)

  • role in early human embryonic development (PMID:12147252)
  • ZNF323 is a schizophrenia susceptibility gene whose expression may influence schizophrenia risk. (PMID:25759474)
  • ZSCAN31 hypermethylation is associated with lung cancer. (PMID:28722770)
  • Functional variants fine-mapping and gene function characterization provide insights into the role of ZNF323 in schizophrenia pathogenesis. (PMID:33522098)

Cross-species orthologs

0 orthologs

Paralogs (30): ZNF263 (ENSG00000006194), ZNF213 (ENSG00000085644), ZNF500 (ENSG00000103199), ZKSCAN1 (ENSG00000106261), ZNF205 (ENSG00000122386), ZSCAN9 (ENSG00000137185), PGBD1 (ENSG00000137338), ZNF215 (ENSG00000149054), ZSCAN12 (ENSG00000158691), ZNF394 (ENSG00000160908), ZNF75A (ENSG00000162086), ZSCAN21 (ENSG00000166529), ZNF232 (ENSG00000167840), ZNF24 (ENSG00000172466), ZNF449 (ENSG00000173275), ZSCAN4 (ENSG00000180532), ZSCAN22 (ENSG00000182318), ZNF75D (ENSG00000186376), ZNF396 (ENSG00000186496), ZNF397 (ENSG00000186812), ZSCAN30 (ENSG00000186814), ZKSCAN4 (ENSG00000187626), ZSCAN23 (ENSG00000187987), ZKSCAN3 (ENSG00000189298), ZSCAN16 (ENSG00000196812), ZSCAN25 (ENSG00000197037), ZSCAN26 (ENSG00000197062), ZNF165 (ENSG00000197279), ZKSCAN8 (ENSG00000198315), ZNF853 (ENSG00000236609)

Protein

Protein identifiers

Zinc finger and SCAN domain-containing protein 31Q96LW9 (reviewed: Q96LW9)

Alternative names: Zinc finger protein 323

All UniProt accessions (12): Q96LW9, C9IYT1, C9J1X2, C9J423, C9J6S7, C9JAI0, C9JBH3, C9JH14, C9JHB1, C9JIC2, C9JPM5, C9JUE1

UniProt curated annotations — full annotation on UniProt →

Function. May function as a transcription factor. May be involved in the development of multiple embryonic organs.

Subcellular location. Nucleus.

Tissue specificity. Expressed at high levels in the lung, liver, and kidney, while weakly expressed in intestine, brain, muscle, cholecyst, heart, and pancreas.

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

Isoforms (2)

UniProt IDNamesCanonical?
Q96LW9-11yes
Q96LW9-22

RefSeq proteins (8): NP_001128687, NP_001128688, NP_001230170, NP_001230171, NP_001230172, NP_001230173, NP_112161, NP_665916 (=MANE)

Domains & families (InterPro)

IDNameType
IPR003309SCAN_domDomain
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR038269SCAN_sfHomologous_superfamily

Pfam: PF00096, PF02023

UniProt features (23 total): cross-link 7, zinc finger region 6, sequence variant 5, sequence conflict 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96LW9-F167.960.09

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 (7): 191, 205, 215, 250, 358, 14, 149

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 97 (showing top): KOBAYASHI_EGFR_SIGNALING_24HR_UP, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, ELK1_01, KIM_WT1_TARGETS_12HR_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_UP, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, VERHAAK_GLIOBLASTOMA_NEURAL, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, ATF2_UP.V1_DN, NOTCH_DN.V1_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CAVIN1_TARGET_GENES, CBX5_TARGET_GENES

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transition metal ion binding1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

488 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZSCAN31NKAPLQ5M9Q1512
ZSCAN31CCDC38Q502W7444
ZSCAN31ARMC2Q8NEN0375
ZSCAN31C3orf62Q6ZUJ4374
ZSCAN31AS3MTQ9HBK9368
ZSCAN31KNCNA6PVL3357
ZSCAN31GSTCDQ8NEC7350
ZSCAN31TSPAN18Q96SJ8348
ZSCAN31BEND4Q6ZU67336
ZSCAN31OR1C1Q15619328
ZSCAN31GLT8D1Q68CQ7325
ZSCAN31ZNF804AQ7Z570324
ZSCAN31SPATA9Q9BWV2323
ZSCAN31MPV17LQ2QL34323
ZSCAN31H3BMD7H3BMD7310

IntAct

7 interactions, top by confidence:

ABTypeScore
ZSCAN31DHX57psi-mi:“MI:0914”(association)0.530
CCL1ZSCAN31psi-mi:“MI:0915”(physical association)0.370
DDIT3ZSCAN31psi-mi:“MI:0915”(physical association)0.370
ZSCAN31PDCD11psi-mi:“MI:0914”(association)0.350
ZSCAN31IPO8psi-mi:“MI:0914”(association)0.350
TGIF2ZNF213psi-mi:“MI:0914”(association)0.350

BioGRID (27): MTMR4 (Affinity Capture-MS), PIP5K1A (Affinity Capture-MS), CDKN2AIP (Affinity Capture-MS), DHX57 (Affinity Capture-MS), THAP11 (Affinity Capture-MS), LENG8 (Affinity Capture-MS), RPL26L1 (Affinity Capture-MS), TRMT1L (Affinity Capture-MS), YTHDC2 (Affinity Capture-MS), PDCD11 (Affinity Capture-MS), BBX (Affinity Capture-MS), DHX57 (Affinity Capture-MS), PIP5K1A (Affinity Capture-MS), MTMR4 (Affinity Capture-MS), LENG8 (Affinity Capture-MS)

ESM2 similar proteins: A1YEP8, A1YEV9, A1YFW2, A1YG26, A1YG48, A1YG60, A2T6E3, A2T6V8, A2T712, A2T736, A2T7D2, A2T7F4, A2T7L7, A2T812, A6QNZ0, O14709, O15535, O43296, O43309, P10073, P17023, P17097, P49910, Q07231, Q12901, Q15776, Q16670, Q1LZ87, Q3MJ62, Q53GI3, Q571J5, Q5JNZ3, Q5RAE6, Q5RBX0, Q5RCD9, Q5RJ54, Q7Z7L9, Q86W11, Q8IZ26, Q8NF99

Diamond homologs: A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A1YGK6, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736, A2T7D2, A2T7D7, A2T7F2, A2T7F4, A2T7L7, A2T812, A6QNZ0, A6QPT6, B2KFW1, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P10073, P17022, P17028, P17029, P17040, P28698, P49910, P51815, P59923

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance33
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1387 predictions. Top by Δscore:

VariantEffectΔscore
6:28326851:CCAT:Cacceptor_gain1.0000
6:28326852:CAT:Cacceptor_gain1.0000
6:28326852:CATC:Cacceptor_gain1.0000
6:28326854:TCTGG:Tacceptor_loss1.0000
6:28326855:C:CCacceptor_gain1.0000
6:28327379:TTA:Tdonor_loss1.0000
6:28327380:TA:Tdonor_loss1.0000
6:28327381:A:ACdonor_gain1.0000
6:28327381:ACC:Adonor_loss1.0000
6:28327382:C:CCdonor_gain1.0000
6:28327420:T:Cdonor_gain1.0000
6:28327530:GAGCC:Gacceptor_gain1.0000
6:28327531:AGC:Aacceptor_gain1.0000
6:28327531:AGCC:Aacceptor_gain1.0000
6:28327532:GC:Gacceptor_gain1.0000
6:28327532:GCC:Gacceptor_gain1.0000
6:28327533:CC:Cacceptor_gain1.0000
6:28327533:CCT:Cacceptor_gain1.0000
6:28327534:C:CCacceptor_gain1.0000
6:28327542:A:Tacceptor_gain1.0000
6:28350864:GCTT:Gdonor_gain1.0000
6:28327381:AC:Adonor_gain0.9900
6:28327382:CC:Cdonor_gain0.9900
6:28327382:CCTTG:Cdonor_gain0.9900
6:28327529:GGAGC:Gacceptor_gain0.9900
6:28327530:GAGC:Gacceptor_gain0.9900
6:28327534:C:CAacceptor_gain0.9900
6:28327534:C:Tacceptor_gain0.9900
6:28327535:T:Cacceptor_gain0.9900
6:28327541:CAGG:Cacceptor_gain0.9900

AlphaMissense

2697 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:28326475:G:CF304L0.998
6:28326475:G:TF304L0.998
6:28326477:A:GF304L0.998
6:28326559:G:CF276L0.998
6:28326559:G:TF276L0.998
6:28326561:A:GF276L0.998
6:28326307:G:CF360L0.995
6:28326307:G:TF360L0.995
6:28326309:A:GF360L0.995
6:28326391:G:CF332L0.995
6:28326391:G:TF332L0.995
6:28326393:A:GF332L0.995
6:28326643:G:CF248L0.995
6:28326643:G:TF248L0.995
6:28326645:A:GF248L0.995
6:28326280:A:CH369Q0.993
6:28326280:A:TH369Q0.993
6:28326364:A:CH341Q0.992
6:28326364:A:TH341Q0.992
6:28326436:G:CH317Q0.991
6:28326436:G:TH317Q0.991
6:28326450:G:CH313D0.991
6:28326520:G:CH289Q0.991
6:28326520:G:TH289Q0.991
6:28326527:C:GR287P0.991
6:28326604:G:CH261Q0.991
6:28326604:G:TH261Q0.991
6:28326223:A:CF388L0.990
6:28326223:A:TF388L0.990
6:28326225:A:GF388L0.990

dbSNP variants (sampled 300 via entrez): RS1000006131 (6:28344466 C>G), RS1000103709 (6:28354337 G>A), RS1000153942 (6:28330643 A>T), RS1000194106 (6:28330940 A>C), RS1000224610 (6:28331033 A>G), RS1000327745 (6:28346646 G>A), RS1000374837 (6:28338925 C>T), RS1000579281 (6:28333416 C>T), RS1000612277 (6:28346156 T>G), RS1000649330 (6:28331481 T>C), RS1000934909 (6:28332924 A>C), RS1001349275 (6:28327248 T>C), RS1001504420 (6:28356306 T>C), RS1001555425 (6:28348272 A>G), RS1001681080 (6:28354299 T>C)

Disease associations

OMIM: gene MIM:610794 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

30 associations (top):

StudyTraitp-value
GCST001251_11Pulmonary function2.000000e-10
GCST003997_12Myopia1.000000e-12
GCST004521_112Autism spectrum disorder or schizophrenia3.000000e-26
GCST004521_115Autism spectrum disorder or schizophrenia3.000000e-16
GCST004521_166Autism spectrum disorder or schizophrenia4.000000e-24
GCST004521_212Autism spectrum disorder or schizophrenia5.000000e-14
GCST004521_23Autism spectrum disorder or schizophrenia2.000000e-11
GCST004521_43Autism spectrum disorder or schizophrenia2.000000e-27
GCST004521_6Autism spectrum disorder or schizophrenia2.000000e-15
GCST004521_7Autism spectrum disorder or schizophrenia2.000000e-15
GCST004521_73Autism spectrum disorder or schizophrenia8.000000e-11
GCST004521_77Autism spectrum disorder or schizophrenia1.000000e-19
GCST004748_92Lung cancer2.000000e-12
GCST004749_74Lung cancer in ever smokers7.000000e-10
GCST004946_75Schizophrenia5.000000e-36
GCST007559_16Sleep duration (short sleep)4.000000e-09
GCST008921_4Asthma and major depressive disorder2.000000e-11
GCST008921_6Asthma and major depressive disorder1.000000e-09
GCST008972_17Urate levels7.000000e-15
GCST009600_116Anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, or Tourette syndrome (pleiotropy)1.000000e-27
GCST010002_50Refractive error4.000000e-34
GCST010142_16Fish- and plant-related diet2.000000e-10
GCST010142_19Fish- and plant-related diet4.000000e-10
GCST010142_34Fish- and plant-related diet7.000000e-09
GCST010142_35Fish- and plant-related diet8.000000e-09
GCST010142_42Fish- and plant-related diet1.000000e-08
GCST010142_7Fish- and plant-related diet3.000000e-12
GCST010204_199Low density lipoprotein cholesterol levels4.000000e-16
GCST010702_75Subcortical volume (MOSTest)3.000000e-11
GCST010703_272Brain morphology (MOSTest)7.000000e-16

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0003892pulmonary function measurement
EFO:0004314forced expiratory volume
EFO:0004531urate measurement
EFO:0008111diet measurement
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, affects cotreatment, decreases expression8
sodium arseniteaffects expression, affects splicing, increases expression3
trichostatin Adecreases expression, affects expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Cadmium Chlorideincreases expression2
p-Chloromercuribenzoic Aciddecreases expression, affects cotreatment2
aristolochic acid Iincreases expression1
GSK-J4decreases expression1
TAK-243increases sumoylation1
sotorasibaffects cotreatment, increases expression1
methylmercuric chloridedecreases expression1
bisphenol Aaffects cotreatment, decreases methylation1
geraniolincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
cobaltous chlorideincreases expression1
butyraldehydedecreases expression1
ferrous chloridedecreases expression1
coumarinincreases phosphorylation1
S-(1,2-dichlorovinyl)cysteineincreases expression, affects response to substance1
pentanaldecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangaffects cotreatment, decreases expression1
trametinibaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
NVP-BKM120increases expression, affects cotreatment1
Irinotecandecreases expression1
Arsenic Trioxideincreases expression1

Clinical trials (associated diseases)

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