H1-6

gene
On this page

Also known as H1t

Summary

H1-6 (H1.6 linker histone, cluster member, HGNC:4720) is a protein-coding gene on chromosome 6p22.2, encoding Histone H1t (P22492). Testis-specific histone H1 that forms less compacted chromatin compared to other H1 histone subtypes.

Histones are basic nuclear proteins responsible for nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H1 family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6.

Source: NCBI Gene 3010 — RefSeq curated summary.

At a glance

  • GWAS associations: 38
  • Clinical variants (ClinVar): 96 total
  • MANE Select transcript: NM_005323

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4720
Approved symbolH1-6
NameH1.6 linker histone, cluster member
Location6p22.2
Locus typegene with protein product
StatusApproved
AliasesH1t
Ensembl geneENSG00000187475
Ensembl biotypeprotein_coding
OMIM142712
Entrez3010

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000338379

RefSeq mRNA: 1 — MANE Select: NM_005323 NM_005323

CCDS: CCDS34349

Canonical transcript exons

ENST00000338379 — 1 exons

ExonStartEnd
ENSE000013797222610741226108135

Expression profiles

Bgee: expression breadth broad, 50 present calls, max score 87.71.

FANTOM5 (CAGE): breadth broad, TPM avg 5.0806 / max 2730.4174, expressed in 403 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
723065.0806403

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.71gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099177.80gold quality
monocyteCL:000057661.00gold quality
leukocyteCL:000073858.76gold quality
bone marrow cellCL:000209258.26silver quality
endometrium epitheliumUBERON:000481157.27gold quality
upper leg skinUBERON:000426256.90silver quality
metanephric glomerulusUBERON:000473655.97gold quality
corpus callosumUBERON:000233654.45gold quality
frontal poleUBERON:000279550.41gold quality
middle frontal gyrusUBERON:000270250.30gold quality
paraflocculusUBERON:000535150.18gold quality
Brodmann (1909) area 10UBERON:001354150.18gold quality
bloodUBERON:000017849.46gold quality
cerebellar vermisUBERON:000472049.25gold quality
testisUBERON:000047346.21gold quality
left testisUBERON:000453345.65gold quality
quadriceps femorisUBERON:000137744.95gold quality
vastus lateralisUBERON:000137944.01gold quality
bone marrowUBERON:000237143.95gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451143.37gold quality
right testisUBERON:000453443.01gold quality
granulocyteCL:000009442.72silver quality
secondary oocyteCL:000065542.57gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450242.57gold quality
thymusUBERON:000237042.23gold quality
biceps brachiiUBERON:000150742.13gold quality
oviduct epitheliumUBERON:000480441.74gold quality
superficial temporal arteryUBERON:000161441.33gold quality
esophagus squamous epitheliumUBERON:000692041.12gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.13

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): FOXC1, HOXD13, OVOL2, PAX1, PAX3, RFX1, RFX2, RFX4, SP1, SP3

Literature-anchored findings (GeneRIF, showing 1)

  • These results suggested that the testis-specific linker histone, H1T, possesses a specific function to produce the chromatin architecture required for proper chromosome regulation, such as homologous recombination. (PMID:26757249)

Cross-species orthologs

23 orthologs

OrganismSymbolGene ID
danio_reriosi:dkey-261m9.12ENSDARG00000032637
danio_reriohisth1l1ENSDARG00000035519
danio_reriosi:ch211-113a14.24ENSDARG00000051718
danio_reriosi:ch211-113a14.18ENSDARG00000051735
danio_reriozgc:110425ENSDARG00000058479
danio_reriosi:dkey-108k21.10ENSDARG00000075508
danio_reriozgc:163061ENSDARG00000075538
danio_rerioENSDARG00000076766
danio_reriozgc:110216ENSDARG00000077456
danio_reriosi:ch211-103n10.5ENSDARG00000077504
danio_reriosi:dkey-108k21.21ENSDARG00000091905
danio_reriozgc:153405ENSDARG00000096992
danio_reriosi:dkey-23a13.17ENSDARG00000105328
danio_reriohisth1l2ENSDARG00000105350
danio_reriosi:ch73-368j24.11ENSDARG00000105430
danio_reriosi:dkey-108k21.14ENSDARG00000110841
danio_reriohisth1l3ENSDARG00000115766
mus_musculusH1f6ENSMUSG00000036211
caenorhabditis_elegansWBGENE00001853
caenorhabditis_elegansWBGENE00001854
caenorhabditis_elegansWBGENE00001855
caenorhabditis_eleganshil-5WBGENE00001856
caenorhabditis_elegansWBGENE00001857

Paralogs (9): H1-3 (ENSG00000124575), H1-1 (ENSG00000124610), H1-4 (ENSG00000168298), H1-8 (ENSG00000178804), H1-5 (ENSG00000184357), H1-10 (ENSG00000184897), H1-7 (ENSG00000187166), H1-2 (ENSG00000187837), H1-0 (ENSG00000189060)

Protein

Protein identifiers

Histone H1tP22492 (reviewed: P22492)

Alternative names: Testicular H1 histone

All UniProt accessions (1): P22492

UniProt curated annotations — full annotation on UniProt →

Function. Testis-specific histone H1 that forms less compacted chromatin compared to other H1 histone subtypes. Formation of more relaxed chromatin may be required to promote chromatin architecture required for proper chromosome regulation during meiosis, such as homologous recombination. Histones H1 act as linkers that bind to nucleosomes and compact polynucleosomes into a higher-order chromatin configuration.

Subcellular location. Nucleus. Chromosome.

Tissue specificity. Testis-specific.

Post-translational modifications. Phosphorylated in early spermatids. Citrullination at Arg-58 (H1R54ci) by PADI4 takes place within the DNA-binding site of H1 and results in its displacement from chromatin and global chromatin decondensation, thereby promoting pluripotency and stem cell maintenance. Deamidation of Asn-80 and Asn-81 by CTPS1 in response to DNA damage promotes subsequent acetylation of histone H1 at Lys-79 (H1K75ac). Acetylated at Lys-79 (H1K75ac) by EP300 following deamidation of Asn-80 and Asn-81 by CTPS1 in response to DNA damage, thereby increasing chromatin accessibility to facilitate the recruitment of DNA repair proteins.

Similarity. Belongs to the histone H1/H5 family.

RefSeq proteins (1): NP_005314* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR005818Histone_H1/H5_H15Domain
IPR005819H1/H5Family
IPR036388WH-like_DNA-bd_sfHomologous_superfamily
IPR036390WH_DNA-bd_sfHomologous_superfamily

Pfam: PF00538

UniProt features (31 total): modified residue 18, compositionally biased region 4, sequence variant 3, region of interest 2, initiator methionine 1, chain 1, domain 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P22492-F163.530.30

Functional residue map

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

Catalytic / active sites (1): 56 (important for nucleosome binding properties)

Post-translational modifications (18): 9, 38, 58, 67, 68, 79, 80, 81, 89, 94, 94, 110, 143, 159, 162, 166, 181, 190

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 83 (showing top): GOBP_CHROMOSOME_ORGANIZATION, GOBP_REGULATION_OF_DNA_RECOMBINATION, GOBP_NEGATIVE_REGULATION_OF_DNA_RECOMBINATION, GOBP_MALE_GAMETE_GENERATION, GOBP_CHROMOSOME_CONDENSATION, HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_DN, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, GFI1_01, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, MODULE_203, GOBP_PROTEIN_DNA_COMPLEX_ORGANIZATION, LEE_AGING_CEREBELLUM_DN, GOBP_CHROMATIN_REMODELING, MEF2_Q6_01, TTTNNANAGCYR_UNKNOWN

GO Biological Process (5): nucleosome assembly (GO:0006334), spermatogenesis (GO:0007283), cell differentiation (GO:0030154), chromosome condensation (GO:0030261), negative regulation of DNA recombination (GO:0045910)

GO Molecular Function (5): double-stranded DNA binding (GO:0003690), structural constituent of chromatin (GO:0030527), nucleosomal DNA binding (GO:0031492), DNA binding (GO:0003677), chromatin DNA binding (GO:0031490)

GO Cellular Component (4): nucleosome (GO:0000786), nucleus (GO:0005634), chromatin (GO:0000785), chromosome (GO:0005694)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA binding2
chromatin2
chromatin organization1
nucleosome organization1
protein-DNA complex assembly1
developmental process involved in reproduction1
male gamete generation1
cellular developmental process1
chromosome organization1
regulation of DNA recombination1
DNA recombination1
negative regulation of DNA metabolic process1
structural molecule activity1
chromatin DNA binding1
nucleosome binding1
nucleic acid binding1
chromatin binding1
protein-DNA complex1
intracellular membrane-bounded organelle1
chromosome1
cellular anatomical structure1
intracellular membraneless organelle1

Protein interactions and networks

STRING

998 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
H1-6H1-8Q8IZA3976
H1-6H1-7Q75WM6955
H1-6H1-10Q92522903
H1-6NASPP49321791
H1-6SLBPQ14493738
H1-6SYCP3Q8IZU3690
H1-6DHX29Q7Z478653
H1-6H3-4Q16695626
H1-6SYCP1Q15431621
H1-6RPS20P17075593
H1-6RPS3P23396552
H1-6RPS26P02383544
H1-6TNP2Q05952541
H1-6SPO11Q9Y5K1528
H1-6H2BC1Q96A08527
H1-6H1-4P10412527

IntAct

89 interactions, top by confidence:

ABTypeScore
H2AXPPM1Gpsi-mi:“MI:0914”(association)0.730
UBASH3BEGFRpsi-mi:“MI:0914”(association)0.690
H2AC4PPM1Gpsi-mi:“MI:0914”(association)0.670
H2BC1PPM1Gpsi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
MECP2KPNA3psi-mi:“MI:0914”(association)0.640
OPG200IKBKBpsi-mi:“MI:0914”(association)0.620
YWHAZLMNApsi-mi:“MI:0914”(association)0.560
MECP2GTPBP10psi-mi:“MI:0914”(association)0.530
NPDC1TCAF2psi-mi:“MI:0914”(association)0.530
H1-6ZNF724psi-mi:“MI:0914”(association)0.530
ZNF71NVLpsi-mi:“MI:0914”(association)0.530
BHLHA15RPLP0psi-mi:“MI:0914”(association)0.530
NRBM47psi-mi:“MI:0914”(association)0.530
THAP3CASC3psi-mi:“MI:0914”(association)0.530
H2BC26PPM1Gpsi-mi:“MI:0914”(association)0.530
H2AC20PPM1Gpsi-mi:“MI:0914”(association)0.530
RPL7ANVLpsi-mi:“MI:0914”(association)0.530
P/V/CKPNA3psi-mi:“MI:0914”(association)0.530
TSC22D1KRT1psi-mi:“MI:0914”(association)0.460
H1-6H2BC15psi-mi:“MI:0915”(physical association)0.400

BioGRID (310): HIST1H1T (Affinity Capture-MS), HIST1H1T (Affinity Capture-MS), HIST1H1T (Proximity Label-MS), HIST1H1T (Affinity Capture-MS), HIST1H1T (Affinity Capture-MS), ZC3HAV1 (Affinity Capture-MS), HIST1H1T (Affinity Capture-MS), HIST1H1E (Affinity Capture-MS), HIST1H1T (Affinity Capture-MS), YBX2 (Affinity Capture-MS), TUBA8 (Affinity Capture-MS), RPL30 (Affinity Capture-MS), ELAVL2 (Affinity Capture-MS), HIST1H1T (Affinity Capture-MS), ZNF724P (Affinity Capture-MS)

ESM2 similar proteins: A4FV97, B8QB46, D3Z8Y2, D3ZZW6, P06348, P06349, P0CB48, P22492, P23497, P38432, P40286, P48778, Q07133, Q08DU9, Q0VEE6, Q18336, Q28EG9, Q3TEA8, Q3TYG6, Q3U1C4, Q3V1H1, Q4R8T4, Q5RFC2, Q5RKG3, Q5SSJ5, Q5ZJ20, Q5ZM33, Q61464, Q62187, Q66H19, Q6K0P9, Q6P747, Q75WM6, Q7L190, Q7Z7J5, Q80VM8, Q8BVK9, Q8BVY0, Q8CJI4, Q8VIK3

Diamond homologs: A7MAZ5, D3ZBN0, D3ZZW6, D4A3K5, G3N131, O01833, O16277, P02251, P02252, P02253, P02254, P02255, P02256, P02257, P02258, P02259, P06144, P06348, P06349, P06350, P06513, P06892, P06893, P06894, P07305, P07796, P08284, P08285, P08286, P08287, P08288, P09426, P09987, P10412, P10922, P15796, P15864, P15865, P15866, P15867

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 94 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Replacement of protamines by nucleosomes in the male pronucleus1043.2×2e-12
FXIIa activates plasma kallikrein-kinin system1335.7×1e-14
Packaging Of Telomere Ends1034.9×5e-12
SIRT1 negatively regulates rRNA expression1232.5×3e-13
Recognition and association of DNA glycosylase with site containing an affected purine1032.4×8e-12
Cleavage of the damaged purine1032.4×8e-12
Recognition and association of DNA glycosylase with site containing an affected pyrimidine1132.2×2e-12
Cleavage of the damaged pyrimidine1132.2×2e-12

GO biological processes:

GO termPartnersFoldFDR
heterochromatin formation824.9×3e-07
nucleosome assembly1220.6×3e-10
cytoplasmic translation613.6×7e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance87
Likely benign9
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

192 predictions. Top by Δscore:

VariantEffectΔscore
6:26108012:T:TAdonor_gain0.7800
6:26107911:CATA:Cdonor_loss0.7600
6:26107912:ATACC:Adonor_loss0.7600
6:26107913:TA:Tdonor_loss0.7600
6:26107914:A:AGdonor_loss0.7600
6:26107915:C:CAdonor_loss0.7600
6:26107981:TTGCG:Tdonor_gain0.7500
6:26107997:T:Cdonor_gain0.7500
6:26107909:GACAT:Gdonor_loss0.7400
6:26107910:ACATA:Adonor_loss0.7400
6:26107916:C:Tdonor_loss0.7400
6:26107915:CCTA:Cdonor_gain0.7100
6:26107919:CT:Cdonor_gain0.6900
6:26107569:AC:Adonor_gain0.6700
6:26107570:CC:Cdonor_gain0.6700
6:26107996:A:ACdonor_gain0.6600
6:26107715:A:ACdonor_gain0.6500
6:26107716:C:CCdonor_gain0.6500
6:26107759:CTAAG:Cdonor_gain0.6400
6:26107763:G:Cdonor_gain0.6300
6:26107924:T:Adonor_gain0.6300
6:26107918:A:ACdonor_gain0.6200
6:26107919:C:CCdonor_gain0.6200
6:26107565:GCTTA:Gdonor_loss0.6000
6:26107567:TTACC:Tdonor_loss0.6000
6:26107568:TACCC:Tdonor_loss0.6000
6:26107569:ACCCT:Adonor_loss0.6000
6:26107570:C:CGdonor_loss0.6000
6:26107501:A:Cdonor_gain0.5900
6:26107569:A:ACdonor_gain0.5900

AlphaMissense

1322 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:26107767:A:CF109L0.994
6:26107767:A:TF109L0.994
6:26107769:A:GF109L0.994
6:26107768:A:GF109S0.988
6:26107893:C:AK67N0.985
6:26107893:C:GK67N0.985
6:26107843:A:CI84S0.984
6:26107843:A:GI84T0.983
6:26107831:A:TL88H0.979
6:26107885:A:GL70S0.978
6:26107768:A:CF109C0.976
6:26107846:C:GR83P0.975
6:26107897:A:TL66H0.974
6:26107951:A:CI48S0.974
6:26107804:A:TL97Q0.973
6:26107772:A:GS108P0.969
6:26107897:A:GL66P0.969
6:26107951:A:GI48T0.966
6:26107951:A:TI48N0.965
6:26107831:A:GL88P0.960
6:26107843:A:TI84N0.960
6:26107774:C:TG107D0.958
6:26107789:C:TG102D0.956
6:26107847:G:TR83S0.956
6:26107871:A:CY75D0.952
6:26107783:C:TG104D0.950
6:26107889:C:GA69P0.950
6:26107790:C:GG102R0.949
6:26107894:T:GK67T0.948
6:26107804:A:GL97P0.946

dbSNP variants (sampled 300 via entrez): RS1000644003 (6:26110004 T>G), RS1002618064 (6:26107122 C>CT), RS1004489154 (6:26107997 T>A,C,G), RS1004518794 (6:26108094 A>G), RS1004547727 (6:26107545 C>A,T), RS1005523727 (6:26109466 G>C), RS1007382201 (6:26107314 C>T), RS1008621441 (6:26107186 A>G), RS1009388328 (6:26107071 G>A), RS1009420846 (6:26107208 G>A), RS1009484180 (6:26107280 G>A,T), RS1009803759 (6:26107176 G>A,C), RS1010393876 (6:26107641 C>G,T), RS1011426698 (6:26108246 A>T), RS1012028253 (6:26109425 G>A)

Disease associations

OMIM: gene MIM:142712 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

38 associations (top):

StudyTraitp-value
GCST004003_10Hematocrit1.000000e-08
GCST004004_34Mean corpuscular volume3.000000e-37
GCST004005_11Hemoglobin levels1.000000e-08
GCST004006_19Mean corpuscular hemoglobin3.000000e-31
GCST004007_10Mean corpuscular hemoglobin concentration1.000000e-08
GCST004521_113Autism spectrum disorder or schizophrenia3.000000e-19
GCST004521_169Autism spectrum disorder or schizophrenia4.000000e-14
GCST004521_69Autism spectrum disorder or schizophrenia8.000000e-24
GCST004521_83Autism spectrum disorder or schizophrenia1.000000e-13
GCST004602_48Mean corpuscular volume2.000000e-229
GCST004612_9High light scatter reticulocyte percentage of red cells1.000000e-09
GCST004621_95Red cell distribution width3.000000e-161
GCST004630_84Mean corpuscular hemoglobin0.000000e+00
GCST006011_62Mean corpuscular volume3.000000e-12
GCST006231_29Mean arterial pressure1.000000e-17
GCST007483_46Waist-to-hip ratio adjusted for BMI (additive genetic model)4.000000e-08
GCST007487_27Waist-to-hip ratio adjusted for BMI (additive genetic model)8.000000e-08
GCST007494_7Waist-to-hip ratio adjusted for BMI (additive genetic model)8.000000e-06
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
GCST012226_37Waist circumference adjusted for body mass index3.000000e-09
GCST012227_884Hip circumference adjusted for BMI5.000000e-19
GCST90002383_405Hematocrit3.000000e-178
GCST90002384_81Hemoglobin0.000000e+00
GCST90002385_363High light scatter reticulocyte count3.000000e-69

EFO canonical traits (13, from GWAS)

EFO IDTrait name
EFO:0004348hematocrit
EFO:0004509hemoglobin measurement
EFO:0004527mean corpuscular hemoglobin
EFO:0004528mean corpuscular hemoglobin concentration
EFO:0007986reticulocyte count
EFO:0009188Red cell distribution width
EFO:0006340mean arterial pressure
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008111diet measurement
EFO:0007789BMI-adjusted waist circumference
EFO:0008039BMI-adjusted hip circumference
EFO:0007984platelet component distribution width
EFO:0004305erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
Acetaminophenincreases expression2
Arsenicaffects methylation, affects cotreatment, decreases expression, increases abundance2
pirinixic acidaffects binding, decreases expression, increases activity1
sodium arsenitedecreases expression, increases abundance, affects cotreatment1
manganese chloridedecreases expression, increases abundance, affects cotreatment1
ochratoxin Aincreases expression1
versicolorin Aincreases expression1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, increases expression1
epigallocatechin gallateincreases expression1
2-palmitoylglycerolincreases expression1
abrineincreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
jinfukangaffects cotreatment, decreases expression1
Caffeineincreases expression1
Cisplatinaffects cotreatment, decreases expression1
Hydrogen Peroxidedecreases expression1
Lipopolysaccharidesaffects cotreatment, increases expression1
Manganeseaffects cotreatment, decreases expression, increases abundance1
Rotenonedecreases expression1
Tetrachlorodibenzodioxinincreases expression1
Cyclosporineincreases methylation1
Aflatoxin B1affects expression1
Cadmium Chlorideincreases expression1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.