H1-3

H1.3 linker histone, cluster member, the group of H1 histones

Basic information

Region (hg38): 6:26234211-26234987

Previous symbols: [ "H1F3", "HIST1H1D" ]

Links

ENSG00000124575 ∙ NCBI:3007 ∙ OMIM:142210 ∙ HGNC:4717 ∙ Uniprot:P16402 ∙ 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 H1-3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H1-3 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			44	5		49
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	7	0

Variants in H1-3

This is a list of pathogenic ClinVar variants found in the H1-3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-26234281-G-C		not specified	Uncertain significance (May 06, 2024)
6-26234288-C-G		not specified	Uncertain significance (Jan 08, 2024)
6-26234293-T-C		not specified	Uncertain significance (May 11, 2022)
6-26234303-T-C		not specified	Uncertain significance (Jan 30, 2024)
6-26234327-G-A		not specified	Uncertain significance (Dec 21, 2022)
6-26234332-G-C		not specified	Uncertain significance (Sep 27, 2022)
6-26234350-G-A		not specified	Likely benign (Oct 27, 2022)
6-26234356-G-A		not specified	Uncertain significance (Nov 22, 2023)
6-26234357-C-T		not specified	Uncertain significance (Mar 30, 2024)
6-26234377-GCTT-G			Likely benign (Apr 01, 2023)
6-26234403-C-G		not specified	Uncertain significance (Aug 11, 2022)
6-26234422-A-G		not specified	Uncertain significance (Nov 21, 2022)
6-26234437-G-A		not specified	Uncertain significance (Dec 07, 2021)
6-26234444-T-C		not specified	Likely benign (May 24, 2023)
6-26234455-T-C		not specified	Uncertain significance (Jul 19, 2023)
6-26234464-T-G		not specified	Uncertain significance (Jun 02, 2023)
6-26234476-T-C		not specified	Uncertain significance (May 23, 2023)
6-26234497-G-A		not specified	Uncertain significance (Apr 01, 2024)
6-26234509-A-G		not specified	Likely benign (Feb 01, 2023)
6-26234537-C-T		not specified	Uncertain significance (Jan 29, 2024)
6-26234549-G-A		not specified	Uncertain significance (Jul 31, 2023)
6-26234563-G-C		not specified	Uncertain significance (May 25, 2022)
6-26234564-C-T		not specified	Uncertain significance (Jun 22, 2023)
6-26234570-T-G		not specified	Uncertain significance (Nov 18, 2023)
6-26234578-G-A		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H1-3	protein_coding	protein_coding	ENST00000244534	1	777

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.156	0.650	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-8.06	368	120	3.07	0.00000527	1399
Missense in Polyphen		67	27.272	2.4567		322
Synonymous	-12.3	160	49.6	3.23	0.00000225	487
Loss of Function	0.726	1	2.15	0.466	8.77e-8	54

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: 0.189

Intolerance Scores

• loftool: 0.456
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.11

Haploinsufficiency Scores

• pHI: 0.239
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hist1h1d
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; immune system phenotype; embryo phenotype; reproductive system phenotype; normal 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;nucleosome assembly;regulation of transcription, DNA-templated;nucleosome positioning;chromosome condensation;negative regulation of chromatin silencing;negative regulation of DNA recombination;histone H3-K4 trimethylation;histone H3-K27 trimethylation
• Cellular component: nucleosome;nuclear chromatin;nucleus;nuclear euchromatin
• Molecular function: double-stranded DNA binding;RNA binding;protein binding;chromatin DNA binding;nucleosomal DNA binding