H1-7

Summary

H1-7 (H1.7 linker histone, HGNC:24893) is a protein-coding gene on chromosome 12q13.11, encoding Testis-specific H1 histone (Q75WM6). Essential for normal spermatogenesis and male fertility.

Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is intronless and encodes a replication-independent histone that is a member of the histone H1 family. The related mouse gene encodes a testis specific protein that is required for spermatogenesis and male fertility.

Source: NCBI Gene 341567 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 59 total
• MANE Select transcript: NM_181788

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24893
Approved symbol	H1-7
Name	H1.7 linker histone
Location	12q13.11
Locus type	gene with protein product
Status	Approved
Aliases	HANP1, H1T2
Ensembl gene	ENSG00000187166
Ensembl biotype	protein_coding
OMIM	618565
Entrez	341567

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000335017

RefSeq mRNA: 1 — MANE Select: NM_181788 NM_181788

CCDS: CCDS8762

Canonical transcript exons

ENST00000335017 — 1 exons

Exon	Start	End
ENSE00001331770	48328980	48330279

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 98.08.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	98.08	gold quality
right testis	UBERON:0004534	97.78	gold quality
testis	UBERON:0000473	94.67	gold quality
sperm	CL:0000019	93.15	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.94	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.05	gold quality
adult organism	UBERON:0007023	85.71	gold quality
sural nerve	UBERON:0015488	81.51	gold quality
buccal mucosa cell	CL:0002336	76.65	gold quality
upper arm skin	UBERON:0004263	70.01	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	67.41	gold quality
biceps brachii	UBERON:0001507	64.41	gold quality
nasal cavity epithelium	UBERON:0005384	63.65	gold quality
kidney epithelium	UBERON:0004819	62.61	gold quality
secondary oocyte	CL:0000655	61.70	gold quality
heart right ventricle	UBERON:0002080	61.45	gold quality
vena cava	UBERON:0004087	61.13	gold quality
granulocyte	CL:0000094	59.82	gold quality
lateral nuclear group of thalamus	UBERON:0002736	59.82	gold quality
tendon of biceps brachii	UBERON:0008188	59.17	gold quality
substantia nigra pars compacta	UBERON:0001965	59.11	gold quality
pancreatic ductal cell	CL:0002079	58.81	silver quality
myocardium	UBERON:0002349	58.69	gold quality
parotid gland	UBERON:0001831	58.43	gold quality
quadriceps femoris	UBERON:0001377	57.96	gold quality
vastus lateralis	UBERON:0001379	57.62	gold quality
mucosa of stomach	UBERON:0001199	57.60	gold quality
medial globus pallidus	UBERON:0002477	57.55	gold quality
cerebellar vermis	UBERON:0004720	57.54	gold quality
globus pallidus	UBERON:0001875	57.27	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	31.39
E-ANND-3	no	0.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting H1-7, 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-574-5P	100.00	66.01	989
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-6833-5P	99.50	68.93	1161
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-625-5P	99.02	68.64	2031
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-3190-3P	97.61	66.95	1406

Literature-anchored findings (GeneRIF, showing 2)

• H1T2 is a protein required for proper cell restructuring and DNA condensation during the elongation phase of spermiogenesis. (PMID:15710904)
• h-HANP1 is expressed in the testes and its genomic construct also intronless as mouse Hanp1. We found that the h-HANP1 coding region have 5 single-nucleotide polymorphisms in Japanese men. (PMID:16533358)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
mus_musculus	H1f7	ENSMUSG00000048077
rattus_norvegicus	H1f7	ENSRNOG00000029545
caenorhabditis_elegans		WBGENE00001853
caenorhabditis_elegans		WBGENE00001854
caenorhabditis_elegans		WBGENE00001855
caenorhabditis_elegans	hil-5	WBGENE00001856
caenorhabditis_elegans		WBGENE00001857

Paralogs (9): H1-3 (ENSG00000124575), H1-1 (ENSG00000124610), H1-4 (ENSG00000168298), H1-8 (ENSG00000178804), H1-5 (ENSG00000184357), H1-10 (ENSG00000184897), H1-6 (ENSG00000187475), H1-2 (ENSG00000187837), H1-0 (ENSG00000189060)

Protein

Protein identifiers

Testis-specific H1 histone — Q75WM6 (reviewed: Q75WM6)

Alternative names: Haploid germ cell-specific nuclear protein 1, Histone H1.7, Histone H1t2

All UniProt accessions (2): A0A140VK96, Q75WM6

UniProt curated annotations — full annotation on UniProt →

Function. Essential for normal spermatogenesis and male fertility. Required for proper cell restructuring and DNA condensation during the elongation phase of spermiogenesis. Involved in the histone-protamine transition of sperm chromatin and the subsequent production of functional sperm. Binds both double-stranded and single-stranded DNA, ATP and protamine-1.

Subcellular location. Nucleus. Chromosome.

Tissue specificity. Testis-specific.

Similarity. Belongs to the histone H1/H5 family.

RefSeq proteins (1): NP_861453* (*=MANE)

Domains & families (InterPro)

UniProt features (17 total): sequence variant 6, compositionally biased region 6, region of interest 2, chain 1, sequence conflict 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q75WM6-F1	63.64	0.08

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): 56

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 50 (showing top): GOBP_CHROMOSOME_ORGANIZATION, GOBP_REGULATION_OF_DNA_RECOMBINATION, GOBP_NEGATIVE_REGULATION_OF_DNA_RECOMBINATION, GOBP_MALE_GAMETE_GENERATION, GOBP_CHROMOSOME_CONDENSATION, GOBP_NUCLEUS_ORGANIZATION, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_SPERMATID_NUCLEUS_DIFFERENTIATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOMF_CHROMATIN_BINDING, GOBP_DNA_METABOLIC_PROCESS, GOMF_NUCLEOSOME_BINDING, MATZUK_SPERMATID_DIFFERENTIATION, GOMF_CHROMATIN_DNA_BINDING

GO Biological Process (6): spermatid nucleus elongation (GO:0007290), chromosome condensation (GO:0030261), sperm DNA condensation (GO:0035092), negative regulation of DNA recombination (GO:0045910), spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (6): double-stranded DNA binding (GO:0003690), ATP binding (GO:0005524), nucleosomal DNA binding (GO:0031492), nucleotide binding (GO:0000166), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), chromosome (GO:0005694)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
spermatid nucleus differentiation	2
nucleus organization	1
chromosome organization	1
chromatin organization	1
regulation of DNA recombination	1
DNA recombination	1
negative regulation of DNA metabolic process	1
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
DNA binding	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
chromatin DNA binding	1
nucleosome binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
nucleic acid binding	1
binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

646 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
H1-7	H1-6	P22492	955
H1-7	H1-8	Q8IZA3	948
H1-7	H1-10	Q92522	946
H1-7	H1-1	Q02539	922
H1-7	H1-4	P10412	894
H1-7	H1-5	P16401	891
H1-7	H1-0	P07305	813
H1-7	H1-3	P16402	762
H1-7	H1-2	P16403	730
H1-7	TNP2	Q05952	590
H1-7	PRM2	P04554	571
H1-7	TNP1	P09430	547
H1-7	H2BC1	Q96A08	505
H1-7	H2AC1	Q96QV6	480
H1-7	LELP1	Q5T871	465

IntAct

17 interactions, top by confidence:

A	B	Type	Score
MBLAC1	H1-7	psi-mi:“MI:0914”(association)	0.560
MEOX2	H1-7	psi-mi:“MI:0915”(physical association)	0.560
H1-7	H2BC15	psi-mi:“MI:0915”(physical association)	0.560
MBLAC1	H1-7	psi-mi:“MI:0915”(physical association)	0.560
RNF217	ACTA2	psi-mi:“MI:0914”(association)	0.530
IGFBP1	SUSD5	psi-mi:“MI:0914”(association)	0.530
H1-7		psi-mi:“MI:0914”(association)	0.350
H1-7	PTX3	psi-mi:“MI:0914”(association)	0.350
SDR9C7	H1-7	psi-mi:“MI:0914”(association)	0.350
H1-7	MEOX2	psi-mi:“MI:0915”(physical association)	0.000
H2BC15	H1-7	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (178): H1FNT (Affinity Capture-MS), H1FNT (Affinity Capture-MS), H1FNT (Two-hybrid), HIST1H2BN (Two-hybrid), GSG2 (Affinity Capture-MS), MRPL50 (Affinity Capture-MS), DDX10 (Affinity Capture-MS), TEX10 (Affinity Capture-MS), RBM23 (Affinity Capture-MS), DDX31 (Affinity Capture-MS), HIST1H2AG (Affinity Capture-MS), MRPL38 (Affinity Capture-MS), MRPL40 (Affinity Capture-MS), ZNF22 (Affinity Capture-MS), MRPS18C (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: D4A3K5, P08284, P08286, Q5RKG3, Q75WM6, Q8CJI4, G3N131, P06892, P08287, P08288, P09987, P15865, P43275, A7MAZ5, P02251, P02252, P02253, P06348, P09426, P10412, P15864, P16401, P16402, P16403, P40286, P43274, P43276, P43277, Q02539

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

172 predictions. Top by Δscore:

Variant	Effect	Δscore
12:48329058:GATCA:G	donor_gain	0.7500
12:48329063:G:GG	donor_gain	0.7400
12:48329251:G:T	acceptor_gain	0.6300
12:48329522:A:AG	acceptor_gain	0.6200
12:48329523:G:GG	acceptor_gain	0.6200
12:48329477:G:T	acceptor_gain	0.5600
12:48329063:GT:G	donor_gain	0.5500
12:48329062:A:AG	donor_gain	0.5200
12:48329064:T:TG	donor_gain	0.5100
12:48329061:CAGTA:C	donor_gain	0.5000
12:48329062:AGTA:A	donor_gain	0.5000
12:48329504:CAA:C	acceptor_gain	0.5000
12:48329505:AAA:A	acceptor_gain	0.5000
12:48329065:AAGTT:A	donor_gain	0.4900
12:48329486:C:CA	acceptor_gain	0.4800
12:48329476:A:T	acceptor_gain	0.4700
12:48329066:AGTTT:A	donor_gain	0.4600
12:48329067:GTTTG:G	donor_gain	0.4600
12:48329506:A:AC	acceptor_gain	0.4500
12:48329234:AGG:A	acceptor_gain	0.4200
12:48329514:ACTCT:A	acceptor_loss	0.4200
12:48329518:TGGCA:T	acceptor_loss	0.4200
12:48329519:GGCAG:G	acceptor_loss	0.4200
12:48329520:GCAG:G	acceptor_loss	0.4200
12:48329521:CAGC:C	acceptor_loss	0.4200
12:48329522:A:T	acceptor_loss	0.4200
12:48329523:G:GA	acceptor_loss	0.4200
12:48329515:CTCT:C	acceptor_loss	0.4100
12:48329068:T:TA	donor_gain	0.4000
12:48329072:ATTTG:A	donor_gain	0.4000

AlphaMissense

1618 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:48329649:T:C	F120L	0.948
12:48329651:C:A	F120L	0.948
12:48329651:C:G	F120L	0.948
12:48329527:T:A	L79H	0.928
12:48329494:T:C	I68T	0.927
12:48329650:T:C	F120S	0.925
12:48329494:T:A	I68N	0.921
12:48329490:G:C	A67P	0.918
12:48329656:T:A	V122D	0.918
12:48329547:G:C	A86P	0.902
12:48329554:A:C	Y88S	0.902
12:48329553:T:C	Y88H	0.901
12:48329482:T:A	V64E	0.898
12:48329617:T:A	L109H	0.890
12:48329494:T:G	I68S	0.887
12:48329551:G:T	G87V	0.883
12:48329553:T:G	Y88D	0.880
12:48329625:A:C	S112R	0.879
12:48329627:C:A	S112R	0.879
12:48329627:C:G	S112R	0.879
12:48329539:T:C	L83P	0.873
12:48329527:T:C	L79P	0.860
12:48329473:C:T	S61F	0.859
12:48329623:T:A	V111D	0.847
12:48329620:G:C	R110P	0.837
12:48329539:T:A	L83H	0.835
12:48329531:G:C	K80N	0.833
12:48329531:G:T	K80N	0.833
12:48329472:T:C	S61P	0.831
12:48329515:C:T	T75I	0.829

dbSNP variants (sampled 300 via entrez): RS1000417144 (12:48330441 A>G), RS1000650905 (12:48328320 G>A), RS1001919887 (12:48329736 G>C), RS1003343737 (12:48328407 A>C), RS1003443892 (12:48328088 T>A,C), RS1004289748 (12:48326995 C>T), RS1005292381 (12:48328323 T>C), RS1007764845 (12:48330562 C>T), RS1009315581 (12:48330491 G>A), RS1009670457 (12:48329766 C>T), RS1011139294 (12:48327265 T>A,C), RS1012177545 (12:48328557 T>G), RS1013601087 (12:48329768 G>A,T), RS1015075521 (12:48328853 G>A,T), RS1016444069 (12:48330200 C>T)

Disease associations

OMIM: gene MIM:618565 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST006629_37	Pulse pressure	3.000000e-21
GCST007267_309	Systolic blood pressure	4.000000e-10
GCST007269_50	Pulse pressure	3.000000e-18

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005763	pulse pressure measurement
EFO:0006335	systolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
2-palmitoylglycerol	increases expression	1
clothianidin	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
p-Chloromercuribenzoic Acid	increases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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