H1-6

H1.6 linker histone, cluster member, the group of H1 histones

Basic information

Region (hg38): 6:26107411-26108135

Previous symbols: [ "H1FT", "HIST1H1T" ]

Links

ENSG00000187475 ∙ NCBI:3010 ∙ OMIM:142712 ∙ HGNC:4720 ∙ Uniprot:P22492 ∙ 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 H1-6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H1-6 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			33	3		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	3	0

Variants in H1-6

This is a list of pathogenic ClinVar variants found in the H1-6 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-26107486-G-C		not specified	Uncertain significance (Apr 12, 2023)
6-26107526-A-G		not specified	Likely benign (Jul 30, 2023)
6-26107528-T-C		not specified	Uncertain significance (May 01, 2023)
6-26107531-G-A		not specified	Uncertain significance (Feb 28, 2024)
6-26107550-G-A		not specified	Uncertain significance (Jun 26, 2023)
6-26107552-C-T		not specified	Uncertain significance (Mar 19, 2024)
6-26107565-G-T		not specified	Uncertain significance (Jan 05, 2022)
6-26107618-G-C		not specified	Uncertain significance (Jul 30, 2023)
6-26107624-C-T		not specified	Uncertain significance (Mar 29, 2024)
6-26107668-C-G		not specified	Uncertain significance (Oct 05, 2021)
6-26107676-C-A		not specified	Uncertain significance (Jul 19, 2023)
6-26107736-T-C		not specified	Uncertain significance (May 10, 2024)
6-26107745-G-A		not specified	Uncertain significance (Dec 27, 2023)
6-26107750-A-G		not specified	Likely benign (Mar 20, 2024)
6-26107757-T-C		not specified	Uncertain significance (Jul 30, 2023)
6-26107760-T-C		not specified	Uncertain significance (Jun 23, 2023)
6-26107765-T-C		not specified	Uncertain significance (Sep 17, 2021)
6-26107820-C-T		not specified	Uncertain significance (Jun 24, 2022)
6-26107846-C-T		not specified	Uncertain significance (Apr 12, 2023)
6-26107855-T-C		not specified	Uncertain significance (Nov 22, 2023)
6-26107868-C-G		not specified	Uncertain significance (Sep 14, 2022)
6-26107879-G-A		not specified	Uncertain significance (Jul 19, 2023)
6-26107888-G-A		not specified	Uncertain significance (Apr 14, 2022)
6-26107912-A-G		not specified	Uncertain significance (Dec 05, 2022)
6-26107913-T-C		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H1-6	protein_coding	protein_coding	ENST00000338379	1	725

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-6.10	293	112	2.62	0.00000638	1311
Missense in Polyphen		72	33.79	2.1308		392
Synonymous	-9.08	128	48.0	2.67	0.00000324	444
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Testis-specific histone H1 that forms less compacted chromatin compared to other H1 histone subtypes (PubMed:26757249). Formation of more relaxed chromatin may be required to promote chromatin architecture required for proper chromosome regulation during meiosis, such as homologous recombination (PubMed:26757249). Histones H1 act as linkers that bind to nucleosomes and compact polynucleosomes into a higher-order chromatin configuration (Probable). {ECO:0000269|PubMed:26757249, ECO:0000305}.

Recessive Scores

• pRec: 0.162

Intolerance Scores

• loftool: 0.826
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.87

Haploinsufficiency Scores

• pHI: 0.0349

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.676

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hist1h1t
• Phenotype: reproductive system phenotype; normal phenotype

Gene ontology

• Biological process: nucleosome assembly;regulation of transcription, DNA-templated;multicellular organism development;spermatogenesis;binding of sperm to zona pellucida;nucleosome positioning;cell differentiation;chromosome condensation;flagellated sperm motility;negative regulation of chromatin silencing;negative regulation of DNA recombination
• Cellular component: nucleosome;condensed nuclear chromosome;nucleus
• Molecular function: double-stranded DNA binding;protein binding;nucleosomal DNA binding