H3C13

H3 clustered histone 13, the group of H3 histones

Basic information

Region (hg38): 1:149813225-149813693

Previous symbols: [ "HIST2H3D" ]

Links

ENSG00000183598 ∙ NCBI:653604 ∙ ∙ HGNC:25311 ∙ Uniprot:Q71DI3 ∙ 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 H3C13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H3C13 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					2	2
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	2

Variants in H3C13

This is a list of pathogenic ClinVar variants found in the H3C13 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-149813312-C-T		not specified	Uncertain significance (Aug 03, 2022)
1-149813319-C-T		not specified	Uncertain significance (Nov 13, 2024)
1-149813330-C-T		not specified	Uncertain significance (Jan 26, 2025)
1-149813353-A-T		not specified	Uncertain significance (Nov 21, 2022)
1-149813420-A-G		not specified	Uncertain significance (Sep 17, 2021)
1-149813442-C-G		not specified	Uncertain significance (Jul 05, 2023)
1-149813452-T-A		not specified	Uncertain significance (Apr 26, 2024)
1-149813459-T-C		not specified	Uncertain significance (Sep 02, 2024)
1-149813473-C-T		not specified	Uncertain significance (Nov 03, 2023)
1-149813484-C-T			Benign (Jul 17, 2018)
1-149813508-A-G			Benign (Jul 17, 2018)
1-149813566-G-A		not specified	Uncertain significance (May 24, 2024)
1-149813576-C-T		not specified	Uncertain significance (Mar 03, 2025)
1-149813594-C-A		not specified	Uncertain significance (Feb 04, 2025)
1-149813615-T-C		not specified	Uncertain significance (Jun 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H3C13	protein_coding	protein_coding	ENST00000331491	1	411

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000703	0.321	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.858	110	87.4	1.26	0.00000399	855
Missense in Polyphen		31	30.011	1.0329		317
Synonymous	-5.11	82	40.6	2.02	0.00000185	307
Loss of Function	-0.656	4	2.81	1.42	1.19e-7	33

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: 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.
• Pathway: Systemic lupus erythematosus - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Alcoholism - Homo sapiens (human);Histone Modifications;B-WICH complex positively regulates rRNA expression;ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;SIRT1 negatively regulates rRNA expression;Interleukin-7 signaling;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Signaling by WNT;Signal Transduction;DNA methylation;Epigenetic regulation of gene expression;Gene expression (Transcription);Signaling by Interleukins;Generic Transcription Pathway;Cytokine Signaling in Immune system;Oxidative Stress Induced Senescence;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Factors involved in megakaryocyte development and platelet production;Cellular responses to stress;HDACs deacetylate histones;Metabolism of proteins;Reproduction;HDMs demethylate histones;RNA Polymerase I Promoter Clearance;PKMTs methylate histone lysines;RNA Polymerase I Promoter Opening;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;RMTs methylate histone arginines;Chromatin modifying enzymes;Immune System;RNA Polymerase I Transcription;Amyloid fiber formation;RNA Polymerase I Chain Elongation;Meiotic recombination;Meiosis;Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3;RHO GTPases activate PKNs;HATs acetylate histones;Cellular responses to external stimuli;RHO GTPase Effectors;Signaling by Rho GTPases;Hemostasis;Condensation of Prophase Chromosomes;Signaling by Nuclear Receptors;Chromatin organization;Mitotic Prophase;IL4;M Phase;Estrogen-dependent gene expression;Transcriptional regulation by small RNAs;RUNX1 regulates transcription of genes involved in differentiation of HSCs;Cell Cycle;Cell Cycle, Mitotic;ESR-mediated signaling;Transcriptional regulation by RUNX1;Formation of the beta-catenin:TCF transactivating complex;TCF dependent signaling in response to WNT;Gene Silencing by RNA;PRC2 methylates histones and DNA (Consensus)

Intolerance Scores

• loftool: 0.702
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.272
• ghis: 0.413

Essentials

• essential_gene_CRISPR: E
• 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: Hist1h3c