H1-1

Chr 6

H1.1 linker histone, cluster member

Also known as: H1.1, H1A, H1F1, HIST1, HIST1H1A

NCBI Gene: 3024ENSG00000124610UniProt: Q02539

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. [provided by RefSeq, Aug 2015]

92
ClinVar variants
6
Pathogenic / LP
0.00
pLI score
12
Active trials
Clinical Summary— H1-1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
6 Pathogenic / Likely Pathogenic· 75 VUS of 92 total submissions
💊
Clinical Trials
12 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.98LOEUF
pLI 0.000
Z-score -2.74
OE 2.72 (1.13–1.98)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-3.99Z-score
OE missense 2.01 (1.77–1.99)
249 obs / 124.0 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.2.72 (1.13–1.98)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.2.01 (1.77–1.99)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.2.17
0≤1.21.6
LoF obs/exp: 8 / 2.9Missense obs/exp: 249 / 124.0Syn Z: -6.87

ClinVar Variant Classifications

92 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic5
Likely Pathogenic1
VUS75
Likely Benign11
5
Pathogenic
1
Likely Pathogenic
75
VUS
11
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
5
0
5
Likely Pathogenic
0
0
1
0
1
VUS
0
71
4
0
75
Likely Benign
0
7
2
2
11
Benign
0
0
0
0
0
Total07812292

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

H1-1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Nuclear and nucleolar activity of linker histone variant H1.0.
Kowalski A·Cell Mol Biol Lett
2016Review
Histone H1 variants are differentially expressed and incorporated into chromatin during differentiation and reprogramming to pluripotency.
Terme JM et al.·J Biol Chem
2011
Aspochalasin H1: A New Cyclic Aspochalasin from Hawaiian Plant-Associated Endophytic Fungus Aspergillus sp. FT1307.
Qader M et al.·Molecules
2021
Genome distribution of replication-independent histone H1 variants shows H1.0 associated with nucleolar domains and H1X associated with RNA polymerase II-enriched regions.
Mayor R et al.·J Biol Chem
2015
Role of α-Synuclein Regions in Nucleation and Elongation of Amyloid Fiber Assembly.
Gallardo J et al.·ACS Chem Neurosci
2020
Identification of replication-dependent and replication-independent linker histone complexes: Tpr specifically promotes replication-dependent linker histone stability.
Zhang P et al.·BMC Biochem
2016
Association of surgeon and hospital volume with postoperative mortality after total gastrectomy for gastric cancer: data from 71,307 Japanese patients collected from a nationwide web-based data entry system.
Iwatsuki M et al.·Gastric Cancer
2021Cohort
Mapping of B-cell epitopes recognized by antibodies to histones in subsets of juvenile chronic arthritis.
Stemmer C et al.·Clin Immunol Immunopathol
1995
The role of readily available clinical, laboratory and radiologic findings in distinguishing a/H1N1/2009 influenza from other causes of acute febrile respiratory illness under pandemic conditions.
Karplus R et al.·Isr Med Assoc J
2012
Investigation of the utility of the 1.1B4 cell as a model human beta cell line for study of persistent enteroviral infection.
Chaffey JR et al.·Sci Rep
2021Functional
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Acute Coronary SyndromeNursing

Acute Coronary Syndrome and Acupressure

RECRUITING
NCT06300294Phase NAAbant Izzet Baysal UniversityStarted 2024-10-01
acupressure
PainSatisfaction

Effects of Shotblocker and Manual Pressure on Pain and Satisfaction

NOT YET RECRUITING
NCT06947525Phase NANecmettin Erbakan UniversityStarted 2025-04-28
Manual pressureShotblocker
Aromatherapy

EFFECTS OF CİTRUS AND CLOVE OİL AROMATHERAPY İN OLDER ADULTS

NOT YET RECRUITING
NCT07368374Phase NAMersin UniversityStarted 2026-02-01
Intervention Group 1Intervention Group 2Placebo Control Group
Abdominal Surgery by Laparotomy

Hot Compress Application in Open Abdominal Surgery

RECRUITING
NCT06888154Phase NATC Erciyes UniversityStarted 2025-05-15
compress application with heated saline
Cerebral Palsy (CP)SpasticityMotor Learning

Predictors of Motor İmagery Performance in Cerebral Palsy

NOT YET RECRUITING
NCT07002567Abant Izzet Baysal UniversityStarted 2025-07-04
Implicit motor imageryExplicit motor imagery
Infertility

The Enchanting Symphony of Haptonomy's Impact on Attachment and Spousal Harmony for Women Conceiving Through Infertility Treatment

ENROLLING BY INVITATION
NCT06274138Phase NABaskent UniversityStarted 2024-09-15
haptonomy
Risky BabyMotor DevelopmentSensory Profiles

Are Developmentally At Risky Babies Environmentally Disadvantaged?

NOT YET RECRUITING
NCT07063966Abant Izzet Baysal UniversityStarted 2025-07-03
Acute Myeloid Leukemia, AdultMyelodysplastic Syndromes

First-in-human Study Aiming to Characterize the Safety, Tolerability, Pharmacokinetic and Preliminary Signs of Activity of ABD-3001 in Refractory or Relapsed AML and High Risk MDS Adult Patients

RECRUITING
NCT05601726Phase PHASE1, PHASE2Advanced BioDesignStarted 2022-11-08
ABD-3001ABD-3001
Geriatric Patient Care Improvement

Effect of Postoperative Telehealth Counseling on Recovery and Self-Care in Geriatric Day Surgery Patients

NOT YET RECRUITING
NCT06892769Phase NATC Erciyes UniversityStarted 2025-03-15
telehealth counseling
Digital TechnologyTechnology AddictionInternet Addiction Disorder

The Effect of Health Education Based Laughter Yoga Applied to Adolescents on Stress and Digital Gaming Habits

ACTIVE NOT RECRUITING
NCT07032090Phase NASaglik Bilimleri Universitesi Gulhane Tip FakultesiStarted 2025-03-15
Health educationLaughter Yoga
Motivational InterviewingHealth Care Seeking BehaviorMigrants

The Effect of Motivational Interviewing-Based Health Behavior Training in Chronically Ill Migrant Women

NOT YET RECRUITING
NCT06505707Phase NAKahramanmaraş İstiklal UniversityStarted 2024-07-15
Health Seeking Behavior Training Based on Motivational Interviewing Techniques
Care

he Effect of Care and the Use of Virtual Reality Glasses on Pain and Comfort

RECRUITING
NCT06853821Phase NASakarya UniversityStarted 2025-07-01
Comfort Theory Based CareVirtual Reality Glasses

External Resources

Links to major genomics databases and tools