H1-8

H1.8 linker histone, the group of H1 histones

Basic information

Region (hg38): 3:129543174-129551467

Previous symbols: [ "H1FOO" ]

Links

ENSG00000178804 ∙ NCBI:132243 ∙ ∙ HGNC:18463 ∙ Uniprot:Q8IZA3 ∙ 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 H1-8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H1-8 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			30	9		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	9	0

Variants in H1-8

This is a list of pathogenic ClinVar variants found in the H1-8 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-129543242-C-A		not specified	Uncertain significance (Dec 21, 2023)
3-129543242-C-G		not specified	Uncertain significance (Dec 06, 2021)
3-129543243-G-A		not specified	Uncertain significance (Mar 11, 2024)
3-129543244-A-G		not specified	Uncertain significance (Sep 22, 2023)
3-129543246-A-G		not specified	Uncertain significance (Jan 10, 2023)
3-129543259-C-T		not specified	Uncertain significance (Jan 26, 2022)
3-129543268-C-T		not specified	Uncertain significance (Oct 22, 2021)
3-129543293-A-C		not specified	Uncertain significance (Oct 17, 2023)
3-129543304-C-A		not specified	Uncertain significance (May 20, 2024)
3-129547400-A-C		not specified	Uncertain significance (Dec 13, 2021)
3-129547424-C-T		not specified	Uncertain significance (Nov 29, 2021)
3-129547460-C-A		not specified	Uncertain significance (May 30, 2024)
3-129547463-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-129547508-G-A		not specified	Uncertain significance (Aug 04, 2021)
3-129547511-G-A		not specified	Likely benign (Jan 20, 2023)
3-129547511-G-T		not specified	Uncertain significance (Aug 21, 2023)
3-129547551-C-G		not specified	Likely benign (Jun 09, 2022)
3-129547607-C-T		not specified	Uncertain significance (May 30, 2024)
3-129547618-C-T		not specified	Uncertain significance (Mar 25, 2022)
3-129547633-G-A		not specified	Likely benign (Dec 15, 2023)
3-129547658-G-A		not specified	Likely benign (Oct 13, 2023)
3-129547664-C-A		not specified	Uncertain significance (Apr 07, 2022)
3-129549049-G-A		not specified	Uncertain significance (Oct 12, 2021)
3-129549050-C-T		not specified	Uncertain significance (Oct 06, 2021)
3-129549068-C-T		not specified	Likely benign (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H1-8	protein_coding	protein_coding	ENST00000324382	5	8254

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0696	0.878	125555	0	3	125558	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.367	191	206	0.928	0.0000123	2188
Missense in Polyphen		36	40.493	0.88905		488
Synonymous	-0.591	92	85.1	1.08	0.00000548	736
Loss of Function	1.64	3	8.00	0.375	3.35e-7	120

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)	0.0000280	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a key role in the control of gene expression during oogenesis and early embryogenesis, presumably through the perturbation of chromatin structure. Essential for meiotic maturation of germinal vesicle-stage oocytes. The somatic type linker histone H1c is rapidly replaced by H1oo in a donor nucleus transplanted into an oocyte. The greater mobility of H1oo as compared to H1c may contribute to this rapid replacement and increased instability of the embryonic chromatin structure. The rapid replacement of H1c with H1oo may play an important role in nuclear remodeling (By similarity). {ECO:0000250}.
• Pathway: apoptotic dna-fragmentation and tissue homeostasis (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.604
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.44

Haploinsufficiency Scores

• pHI: 0.0356
• hipred: N
• hipred_score: 0.145
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.798

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: H1foo
• Phenotype: normal phenotype

Gene ontology

• Biological process: nucleosome assembly;regulation of transcription, DNA-templated;nucleosome positioning;chromosome condensation;negative regulation of chromatin silencing;regulation of DNA methylation;negative regulation of DNA recombination;meiotic cell cycle;negative regulation of stem cell differentiation
• Cellular component: nucleosome;female germ cell nucleus;nucleus;nucleolus;cytoplasm;extracellular exosome
• Molecular function: double-stranded DNA binding;protein binding;nucleosomal DNA binding