H1-1

H1.1 linker histone, cluster member, the group of H1 histones

Basic information

Region (hg38): 6:26017032-26017787

Previous symbols: [ "H1F1", "HIST1H1A" ]

Links

ENSG00000124610 ∙ NCBI:3024 ∙ OMIM:142709 ∙ HGNC:4715 ∙ Uniprot:Q02539 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the H1-1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H1-1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	4	0

Variants in H1-1

This is a list of pathogenic ClinVar variants found in the H1-1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-26017093-T-C		not specified	Uncertain significance (Sep 05, 2024)
6-26017130-C-T			Likely benign (Jan 01, 2023)
6-26017144-C-A		not specified	Uncertain significance (Oct 14, 2023)
6-26017145-C-G		not specified	Uncertain significance (Jul 11, 2023)
6-26017180-C-G		not specified	Uncertain significance (Aug 12, 2024)
6-26017189-T-C		not specified	Uncertain significance (Sep 12, 2024)
6-26017192-C-T		not specified	Uncertain significance (May 30, 2023)
6-26017233-T-C		not specified	Uncertain significance (Jul 26, 2024)
6-26017239-G-A		not specified	Uncertain significance (Feb 28, 2024)
6-26017260-T-C		not specified	Uncertain significance (Jul 31, 2024)
6-26017261-T-C		not specified	Uncertain significance (Dec 20, 2023)
6-26017410-A-G		not specified	Uncertain significance (Jun 19, 2024)
6-26017426-C-G		not specified	Uncertain significance (Aug 28, 2024)
6-26017452-C-T		not specified	Uncertain significance (Sep 27, 2022)
6-26017467-C-T		not specified	Uncertain significance (Nov 12, 2021)
6-26017474-T-G		not specified	Likely benign (Aug 12, 2021)
6-26017515-C-T		not specified	Uncertain significance (Jun 30, 2023)
6-26017533-T-A		not specified	Uncertain significance (Jul 14, 2023)
6-26017539-A-G		not specified	Uncertain significance (Dec 28, 2023)
6-26017540-G-A		not specified	Uncertain significance (Nov 17, 2022)
6-26017561-C-T		not specified	Likely benign (Aug 27, 2024)
6-26017575-G-A		not specified	Uncertain significance (Jan 26, 2022)
6-26017578-G-A		not specified	Uncertain significance (Sep 30, 2024)
6-26017585-C-T		not specified	Uncertain significance (Sep 12, 2023)
6-26017591-C-T		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H1-1	protein_coding	protein_coding	ENST00000244573	1	781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.13e-8	0.0228	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.99	249	124	2.01	0.00000720	1354
Missense in Polyphen		54	33.837	1.5959		359
Synonymous	-6.87	121	55.7	2.17	0.00000393	475
Loss of Function	-2.74	8	2.94	2.72	1.24e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber. Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers. Acts also as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation (By similarity). {ECO:0000250}.
• Pathway: Formation of Senescence-Associated Heterochromatin Foci (SAHF);DNA Damage/Telomere Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;Activation of DNA fragmentation factor;Apoptosis induced DNA fragmentation;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.213

Intolerance Scores

• loftool: 0.893
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.06

Haploinsufficiency Scores

• pHI: 0.185
• hipred: Y
• hipred_score: 0.595
• ghis: 0.373

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.977

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hist1h1a
• Phenotype: cellular phenotype; normal phenotype; reproductive system phenotype

Gene ontology

• Biological process: nucleosome assembly;regulation of transcription, DNA-templated;spermatogenesis;nucleosome positioning;chromosome condensation;negative regulation of chromatin silencing;negative regulation of DNA recombination;positive regulation of receptor-mediated endocytosis
• Cellular component: nucleosome;nuclear chromatin;nucleus;nuclear euchromatin;cell surface;vesicle
• Molecular function: double-stranded DNA binding;protein binding;heparin binding;chromatin DNA binding;nucleosomal DNA binding