H1-5

H1.5 linker histone, cluster member, the group of H1 histones

Basic information

Region (hg38): 6:27866792-27867588

Previous symbols: [ "H1F5", "HIST1H1B" ]

Links

ENSG00000184357 ∙ NCBI:3009 ∙ OMIM:142711 ∙ HGNC:4719 ∙ Uniprot:P16401 ∙ 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 H1-5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H1-5 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						0
missense			35			35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	0	0

Variants in H1-5

This is a list of pathogenic ClinVar variants found in the H1-5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-27866863-C-T		not specified	Uncertain significance (Mar 28, 2023)
6-27866868-G-A		not specified	Uncertain significance (May 31, 2023)
6-27866877-G-A		not specified	Uncertain significance (Nov 15, 2024)
6-27866898-G-T		not specified	Uncertain significance (Sep 17, 2021)
6-27866899-C-G		not specified	Uncertain significance (Dec 20, 2023)
6-27866923-G-A		not specified	Uncertain significance (Dec 11, 2024)
6-27866933-C-A		not specified	Uncertain significance (Jan 18, 2023)
6-27866944-C-T		not specified	Uncertain significance (Jun 16, 2023)
6-27866955-T-C		not specified	Uncertain significance (Aug 27, 2024)
6-27866961-G-A		not specified	Uncertain significance (Jul 06, 2021)
6-27866970-G-A		not specified	Uncertain significance (Oct 06, 2024)
6-27866986-T-G		not specified	Uncertain significance (Dec 13, 2022)
6-27866992-C-T		not specified	Uncertain significance (Dec 21, 2023)
6-27866997-T-C		not specified	Uncertain significance (Jul 07, 2024)
6-27867027-T-C		not specified	Uncertain significance (Sep 18, 2024)
6-27867043-C-G		not specified	Uncertain significance (Dec 27, 2023)
6-27867045-G-A		not specified	Uncertain significance (Jun 11, 2024)
6-27867087-G-A		not specified	Uncertain significance (Jan 30, 2024)
6-27867090-C-G		not specified	Uncertain significance (Jun 03, 2024)
6-27867105-G-A		not specified	Uncertain significance (Nov 24, 2024)
6-27867126-G-A		not specified	Uncertain significance (Apr 28, 2023)
6-27867145-C-T		not specified	Uncertain significance (Apr 20, 2024)
6-27867168-G-T		not specified	Uncertain significance (Jan 31, 2025)
6-27867219-G-A		not specified	Uncertain significance (Aug 09, 2021)
6-27867226-T-A		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H1-5	protein_coding	protein_coding	ENST00000331442	1	790

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.575	0.384	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.54	232	122	1.90	0.00000549	1412
Missense in Polyphen		26	21.618	1.2027		286
Synonymous	-7.13	118	52.4	2.25	0.00000258	489
Loss of Function	1.50	0	2.63	0.00	1.09e-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: 0.206

Intolerance Scores

• loftool: 0.153
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.17

Haploinsufficiency Scores

• pHI: 0.276
• hipred: Y
• hipred_score: 0.663

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hist1h1b

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin organization;nucleosome assembly;regulation of transcription, DNA-templated;nucleosome positioning;chromosome condensation;positive regulation of cell growth;negative regulation of chromatin silencing;negative regulation of DNA recombination;protein stabilization;positive regulation of histone H3-K9 methylation;establishment of protein localization to chromatin
• Cellular component: nucleosome;nuclear chromatin;nucleus;nuclear heterochromatin
• Molecular function: double-stranded DNA binding;RNA binding;protein binding;chromatin DNA binding;nucleosomal DNA binding;histone deacetylase binding