H3-5

H3.5 histone, the group of H3 histones

Basic information

Region (hg38): 12:31791185-31792298

Previous symbols: [ "H3F3C" ]

Links

ENSG00000188375 ∙ NCBI:440093 ∙ OMIM:616134 ∙ HGNC:33164 ∙ Uniprot:Q6NXT2 ∙ 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 H3-5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H3-5 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in H3-5

This is a list of pathogenic ClinVar variants found in the H3-5 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-31791781-C-T		not specified	Uncertain significance (Nov 27, 2024)
12-31791815-T-C		not specified	Uncertain significance (Jul 30, 2024)
12-31791866-C-T		not specified	Uncertain significance (Sep 10, 2024)
12-31791884-C-T		not specified	Uncertain significance (May 17, 2023)
12-31791895-G-A		not specified	Uncertain significance (Dec 21, 2021)
12-31791902-C-T		not specified	Uncertain significance (Jan 11, 2023)
12-31791970-G-T		not specified	Uncertain significance (Jun 17, 2024)
12-31791985-A-G		not specified	Uncertain significance (Aug 10, 2021)
12-31792010-G-C		not specified	Uncertain significance (Jun 30, 2023)
12-31792019-C-T		not specified	Uncertain significance (Aug 10, 2023)
12-31792114-C-T		not specified	Uncertain significance (Mar 29, 2022)
12-31792115-G-C		not specified	Uncertain significance (Dec 10, 2024)
12-31792115-G-T		not specified	Uncertain significance (Feb 28, 2023)
12-31792117-G-A		not specified	Uncertain significance (Nov 24, 2024)
12-31792151-G-C		not specified	Uncertain significance (Jan 31, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H3-5	protein_coding	protein_coding	ENST00000340398	1	1053

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	0.391	84	94.7	0.887	0.00000710	849
Missense in Polyphen		13	12.894	1.0082		169
Synonymous	-0.840	46	39.3	1.17	0.00000301	299
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: Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Hominid-specific H3.5/H3F3C preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes. {ECO:0000269|PubMed:21274551}.
• Pathway: Systemic lupus erythematosus - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Alcoholism - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.650
• rvis_EVS: 0.88
• rvis_percentile_EVS: 89.02

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.344

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gm12657

Gene ontology

• Biological process: positive regulation of cell growth
• Cellular component: nucleosome;nucleus;nuclear euchromatin
• Molecular function: protein binding;nucleosomal DNA binding;protein heterodimerization activity