APOBEC3H

apolipoprotein B mRNA editing enzyme catalytic subunit 3H, the group of Apolipoprotein B mRNA editing enzyme catalytic subunits

Basic information

Region (hg38): 22:39097223-39104067

Links

ENSG00000100298 ∙ NCBI:164668 ∙ OMIM:610976 ∙ HGNC:24100 ∙ Uniprot:Q6NTF7 ∙ 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 APOBEC3H gene.

• Inborn genetic diseases (11 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOBEC3H 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				1	1	2
missense			10	1		11
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	2	1

Variants in APOBEC3H

This is a list of pathogenic ClinVar variants found in the APOBEC3H region.

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

Position	Type	Phenotype	Significance	ClinVar
22-39100306-C-T		not specified	Uncertain significance (Jun 07, 2023)
22-39100307-G-A		not specified	Uncertain significance (Mar 20, 2023)
22-39100327-C-T		not specified	Uncertain significance (Mar 01, 2024)
22-39100328-G-A		not specified	Uncertain significance (Sep 27, 2021)
22-39100381-A-T		not specified	Uncertain significance (Aug 02, 2021)
22-39100400-C-T		not specified	Uncertain significance (Feb 05, 2024)
22-39100412-G-T		not specified	Uncertain significance (Nov 07, 2023)
22-39101282-A-G		not specified	Uncertain significance (Oct 27, 2022)
22-39101328-C-T		not specified	Uncertain significance (Jan 31, 2022)
22-39101400-G-T		not specified	Uncertain significance (Jul 11, 2023)
22-39101407-C-T			Benign (Apr 10, 2018)
22-39101408-G-A		not specified	Likely benign (Sep 22, 2023)
22-39101424-A-G		not specified	Uncertain significance (Jul 06, 2021)
22-39101450-G-T		not specified	Uncertain significance (Oct 22, 2021)
22-39101457-G-A		not specified	Likely benign (Sep 16, 2021)
22-39101471-T-A		not specified	Uncertain significance (Jan 24, 2024)
22-39101496-G-C		not specified	Uncertain significance (Jun 24, 2022)
22-39101500-C-T			Likely benign (Mar 01, 2022)
22-39101977-T-G		not specified	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOBEC3H	protein_coding	protein_coding	ENST00000401756	4	6844

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00202	0.919	125540	1	206	125747	0.000823

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0191	127	128	0.995	0.00000820	1305
Missense in Polyphen		33	39.759	0.83001		456
Synonymous	-0.634	58	52.2	1.11	0.00000347	370
Loss of Function	1.53	6	11.6	0.515	6.44e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000542	0.000540
Ashkenazi Jewish	0.00160	0.00159
East Asian	0.000163	0.000163
Finnish	0.00102	0.00102
European (Non-Finnish)	0.00124	0.00123
Middle Eastern	0.000163	0.000163
South Asian	0.000266	0.000261
Other	0.000988	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. The A3H- var/haplotype 2 exhibits antiviral activity against vif-deficient HIV-1. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single- stranded DNA and does not deaminate double-stranded DNA or single- or double-stranded RNA. Exhibits antiviral activity also against T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons. {ECO:0000269|PubMed:16571802, ECO:0000269|PubMed:16920826, ECO:0000269|PubMed:18299330, ECO:0000269|PubMed:18779051, ECO:0000269|PubMed:18827027, ECO:0000269|PubMed:20062055, ECO:0000269|PubMed:21835787, ECO:0000269|PubMed:22457529, ECO:0000269|PubMed:22915799, ECO:0000269|PubMed:23097438}.
• Pathway: Metabolism of RNA;Formation of the Editosome;mRNA Editing: C to U Conversion;mRNA Editing (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.871
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.53

Haploinsufficiency Scores

• pHI: 0.0381
• hipred: N
• hipred_score: 0.169
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0116

Gene Damage Prediction

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

Gene ontology

• Biological process: cytidine deamination;negative regulation of transposition;cytidine to uridine editing;innate immune response;negative regulation of single stranded viral RNA replication via double stranded DNA intermediate;negative regulation of viral process;defense response to virus;DNA cytosine deamination;DNA demethylation
• Cellular component: P-body;nucleus;cytoplasm
• Molecular function: RNA binding;cytidine deaminase activity;protein binding;zinc ion binding