H1-0

H1.0 linker histone, the group of H1 histones

Basic information

Region (hg38): 22:37805228-37807432

Previous symbols: [ "H1FV", "H1F0" ]

Links

ENSG00000189060 ∙ NCBI:3005 ∙ OMIM:142708 ∙ HGNC:4714 ∙ Uniprot:P07305 ∙ 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 H1-0 gene.

• not provided (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H1-0 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				1		1
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	0

Variants in H1-0

This is a list of pathogenic ClinVar variants found in the H1-0 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-37805549-C-T		not specified	Uncertain significance (Apr 14, 2022)
22-37805592-C-T			Likely benign (Apr 01, 2022)
22-37805774-C-G		not specified	Uncertain significance (Jan 24, 2024)
22-37805869-A-G		not specified	Uncertain significance (Oct 17, 2023)
22-37805893-G-A		not specified	Uncertain significance (Dec 22, 2023)
22-37805918-A-G		not specified	Uncertain significance (Jul 14, 2021)
22-37805948-C-A		not specified	Uncertain significance (May 05, 2023)
22-37805969-C-T		not specified	Uncertain significance (Dec 15, 2022)
22-37806022-C-T		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H1-0	protein_coding	protein_coding	ENST00000340857	1	2329

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.643	0.333	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.878	88	114	0.769	0.00000634	1250
Missense in Polyphen		13	25.122	0.51748		303
Synonymous	-1.32	64	51.9	1.23	0.00000320	405
Loss of Function	1.69	0	3.31	0.00	1.37e-7	74

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: Histones H1 are necessary for the condensation of nucleosome chains into higher-order structures. The H1F0 histones are found in cells that are in terminal stages of differentiation or that have low rates of cell division.
• Pathway: apoptotic dna-fragmentation and tissue homeostasis;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: 0.208

Intolerance Scores

• loftool: 0.0891
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.850
• hipred: Y
• hipred_score: 0.775
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: H1f0
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; embryo phenotype; immune system phenotype; hematopoietic system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;apoptotic DNA fragmentation;nucleosome assembly;chromatin silencing;regulation of transcription, DNA-templated;nucleosome positioning;chromosome condensation;negative regulation of chromatin silencing;negative regulation of DNA recombination;positive regulation of transcription regulatory region DNA binding
• Cellular component: nucleosome;nuclear chromatin;nucleus;nucleoplasm;nuclear euchromatin;Golgi apparatus;actin cytoskeleton;nuclear body;transcriptional repressor complex
• Molecular function: AT DNA binding;double-stranded DNA binding;RNA binding;protein binding;chromatin DNA binding;nucleosomal DNA binding