HARBI1

harbinger transposase derived 1, the group of DNA transposon derived genes

Basic information

Region (hg38): 11:46602861-46617909

Previous symbols: [ "C11orf77" ]

Links

ENSG00000180423 ∙ NCBI:283254 ∙ OMIM:615086 ∙ HGNC:26522 ∙ Uniprot:Q96MB7 ∙ 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 HARBI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HARBI1 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			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in HARBI1

This is a list of pathogenic ClinVar variants found in the HARBI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-46603548-C-T		not specified	Uncertain significance (May 07, 2024)
11-46603554-C-A		not specified	Uncertain significance (Apr 18, 2023)
11-46603562-G-A		not specified	Uncertain significance (Jul 09, 2024)
11-46603567-C-T		not specified	Uncertain significance (Apr 08, 2022)
11-46603577-C-T		not specified	Uncertain significance (Aug 10, 2021)
11-46603589-A-C		not specified	Uncertain significance (Feb 18, 2025)
11-46603591-T-C		not specified	Uncertain significance (Jul 11, 2022)
11-46603598-G-A		not specified	Uncertain significance (Dec 17, 2023)
11-46603628-T-C		not specified	Likely benign (Jun 10, 2024)
11-46603673-G-C		not specified	Uncertain significance (Mar 03, 2025)
11-46603765-C-T		not specified	Uncertain significance (Jun 03, 2022)
11-46603766-G-A		not specified	Uncertain significance (Nov 23, 2021)
11-46603786-C-T		not specified	Uncertain significance (Sep 25, 2023)
11-46603838-G-A		not specified	Uncertain significance (Jun 04, 2024)
11-46603888-C-T		not specified	Uncertain significance (May 15, 2023)
11-46615580-T-C		not specified	Uncertain significance (Feb 06, 2024)
11-46615658-G-A		not specified	Uncertain significance (Mar 31, 2024)
11-46615673-C-T		not specified	Uncertain significance (Jun 04, 2024)
11-46615694-T-G		not specified	Uncertain significance (Jan 29, 2024)
11-46615702-A-G		not specified	Uncertain significance (Aug 15, 2024)
11-46615783-T-C		not specified	Uncertain significance (May 03, 2023)
11-46615856-T-C		not specified	Likely benign (Jul 09, 2021)
11-46615858-G-A		not specified	Uncertain significance (Apr 22, 2024)
11-46615961-T-C		not specified	Uncertain significance (Jun 05, 2023)
11-46615969-C-G		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HARBI1	protein_coding	protein_coding	ENST00000326737	2	15049

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000648	0.918	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.365	193	208	0.929	0.0000117	2299
Missense in Polyphen		61	79.871	0.76373		874
Synonymous	-1.15	86	73.5	1.17	0.00000373	704
Loss of Function	1.54	7	13.0	0.538	9.61e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000330	0.000330
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000301	0.000299
Middle Eastern	0.000327	0.000326
South Asian	0.0000653	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity. {ECO:0000269|PubMed:15169610, ECO:0000269|PubMed:18339812, ECO:0000305}.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.329
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.342
• hipred: N
• hipred_score: 0.292
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Harbi1

Gene ontology

• Biological process: nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleus;microtubule organizing center;cytosol;plasma membrane
• Molecular function: nuclease activity;metal ion binding