H1-7

H1.7 linker histone, the group of H1 histones

Basic information

Region (hg38): 12:48328980-48330279

Previous symbols: [ "H1FNT" ]

Links

ENSG00000187166 ∙ NCBI:341567 ∙ OMIM:618565 ∙ HGNC:24893 ∙ Uniprot:Q75WM6 ∙ 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 H1-7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H1-7 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	1		31
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	1	0

Variants in H1-7

This is a list of pathogenic ClinVar variants found in the H1-7 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-48329298-C-G		not specified	Uncertain significance (Jan 23, 2025)
12-48329384-A-C		not specified	Uncertain significance (Jan 28, 2025)
12-48329403-A-G		not specified	Uncertain significance (Apr 25, 2023)
12-48329403-A-T		not specified	Uncertain significance (Aug 17, 2021)
12-48329408-G-C		not specified	Uncertain significance (Mar 01, 2024)
12-48329430-G-A		not specified	Uncertain significance (Jul 12, 2023)
12-48329433-G-A		not specified	Uncertain significance (Jun 13, 2024)
12-48329452-C-T		not specified	Uncertain significance (Aug 28, 2024)
12-48329478-T-A		not specified	Uncertain significance (Jan 02, 2024)
12-48329509-G-A		not specified	Uncertain significance (Jul 11, 2022)
12-48329536-A-C		not specified	Uncertain significance (Sep 30, 2024)
12-48329550-G-A		not specified	Uncertain significance (Nov 14, 2024)
12-48329569-A-T		not specified	Uncertain significance (Feb 12, 2024)
12-48329581-A-C		not specified	Uncertain significance (Oct 13, 2023)
12-48329641-C-T		not specified	Uncertain significance (Jan 03, 2024)
12-48329664-G-T		not specified	Uncertain significance (Dec 13, 2023)
12-48329673-C-T		not specified	Uncertain significance (Feb 19, 2025)
12-48329710-G-A		not specified	Uncertain significance (Aug 02, 2021)
12-48329715-C-G		not specified	Uncertain significance (Jun 29, 2022)
12-48329719-C-A		not specified	Uncertain significance (Jan 30, 2024)
12-48329733-C-T		not specified	Uncertain significance (Jun 10, 2024)
12-48329746-G-A		not specified	Uncertain significance (Oct 21, 2024)
12-48329761-G-A		not specified	Uncertain significance (Nov 08, 2022)
12-48329764-G-A		not specified	Uncertain significance (Nov 14, 2023)
12-48329775-C-T		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H1-7	protein_coding	protein_coding	ENST00000335017	1	1300

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	0.570	158	180	0.880	0.0000129	1575
Missense in Polyphen		28	33.555	0.83444		252
Synonymous	0.954	72	83.1	0.867	0.00000666	554
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: Essential for normal spermatogenesis and male fertility (PubMed:16533358). Required for proper cell restructuring and DNA condensation during the elongation phase of spermiogenesis. Involved in the histone-protamine transition of sperm chromatin and the subsequent production of functional sperm. Binds both double-stranded and single-stranded DNA, ATP and protamine-1. {ECO:0000250|UniProtKB:Q8CJI4, ECO:0000269|PubMed:16533358}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.599
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.46

Haploinsufficiency Scores

• pHI: 0.0438
• hipred: N
• hipred_score: 0.123
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00450

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: H1fnt
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;multicellular organism development;spermatid nucleus elongation;nucleosome positioning;chromosome condensation;negative regulation of chromatin silencing;sperm chromatin condensation;negative regulation of DNA recombination
• Cellular component: nuclear chromatin;nucleus
• Molecular function: double-stranded DNA binding;protein binding;ATP binding;nucleosomal DNA binding