HABP2

hyaluronan binding protein 2

Basic information

Region (hg38): 10:113550836-113589602

Links

ENSG00000148702 ∙ NCBI:3026 ∙ OMIM:603924 ∙ HGNC:4798 ∙ Uniprot:Q14520 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Thyroid cancer, nonmedullary 5	AD	Oncologic	Individuals have been described as being susceptible to nonmedullary thyroid cancer, and awareness may allow early surveillance, diagnosis, and management	Oncologic	26222560

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HABP2 gene.

• Factor VII Marburg I Variant Thrombophilia (100 variants)
• not provided (83 variants)
• Inborn genetic diseases (36 variants)
• Thrombophilia due to thrombin defect;Thyroid cancer, nonmedullary, 5 (2 variants)
• THYROID CANCER, NONMEDULLARY, 5, SUSCEPTIBILITY TO (1 variants)
• not specified (1 variants)
• FACTOR VII-ACTIVATING PROTEASE MARBURG I POLYMORPHISM (1 variants)
• HABP2-related condition (1 variants)
• NRAP-related condition (1 variants)
• Venous thromboembolism, susceptibility to (1 variants)
• Thyroid cancer, nonmedullary, 5 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HABP2 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			12	3	3	18
missense			55	10		65
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region			2	2		4
non coding			32	28	46	106
Total	0	0	100	42	49

Variants in HABP2

This is a list of pathogenic ClinVar variants found in the HABP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-113552847-G-A			Benign (Jan 10, 2019)
10-113553047-AT-A		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jun 14, 2016)
10-113553051-T-C		Factor VII Marburg I Variant Thrombophilia	Likely benign (Feb 14, 2020)
10-113553052-T-C		Factor VII Marburg I Variant Thrombophilia	Benign/Likely benign (Jan 10, 2019)
10-113553057-C-G		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 13, 2018)
10-113553064-G-C		Factor VII Marburg I Variant Thrombophilia	Likely benign (Feb 28, 2019)
10-113553119-A-G		Factor VII Marburg I Variant Thrombophilia	Likely benign (Mar 01, 2024)
10-113553136-G-A		not specified	Uncertain significance (Nov 17, 2022)
10-113553167-C-G		Factor VII Marburg I Variant Thrombophilia	Likely benign (Mar 06, 2018)
10-113553178-G-T		not specified	Uncertain significance (Jan 25, 2023)
10-113553180-C-T		not specified	Uncertain significance (Nov 21, 2022)
10-113553184-C-T		Factor VII Marburg I Variant Thrombophilia	Uncertain significance (Jan 13, 2018)
10-113567180-C-A			Benign (Jan 10, 2019)
10-113567186-G-A			Benign (Jan 10, 2019)
10-113567191-C-G			Benign (Jan 10, 2019)
10-113567281-A-G			Benign (Jan 10, 2019)
10-113567289-C-G			Benign (Jan 10, 2019)
10-113567312-G-A			Benign (Jan 10, 2019)
10-113567325-A-G			Benign (Jan 10, 2019)
10-113567434-A-G			Benign (Jan 10, 2019)
10-113567446-G-C			Likely benign (May 26, 2021)
10-113567499-T-G		not specified	Uncertain significance (Aug 02, 2022)
10-113567502-C-G			Uncertain significance (-)
10-113567504-T-G		not specified	Uncertain significance (Jan 31, 2022)
10-113567514-G-T		Factor VII Marburg I Variant Thrombophilia	Likely benign (Feb 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HABP2	protein_coding	protein_coding	ENST00000351270	13	38766

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.96e-15	0.0547	125050	3	695	125748	0.00278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.43	385	314	1.23	0.0000160	3726
Missense in Polyphen		127	106.93	1.1876		1298
Synonymous	-1.34	140	121	1.16	0.00000683	997
Loss of Function	0.690	25	29.0	0.862	0.00000123	362

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00451	0.00451
Ashkenazi Jewish	0.00616	0.00617
East Asian	0.000382	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00383	0.00382
Middle Eastern	0.000382	0.000381
South Asian	0.000459	0.000457
Other	0.00555	0.00555

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves the alpha-chain at multiple sites and the beta- chain between 'Lys-53' and 'Lys-54' but not the gamma-chain of fibrinogen and therefore does not initiate the formation of the fibrin clot and does not cause the fibrinolysis directly. It does not cleave (activate) prothrombin and plasminogen but converts the inactive single chain urinary plasminogen activator (pro- urokinase) to the active two chain form. Activates coagulation factor VII (PubMed:8827452, PubMed:10754382, PubMed:11217080). May function as a tumor suppressor negatively regulating cell proliferation and cell migration (PubMed:26222560). {ECO:0000269|PubMed:10754382, ECO:0000269|PubMed:11217080, ECO:0000269|PubMed:26222560, ECO:0000269|PubMed:8827452}.
• Disease: DISEASE: Thyroid cancer, non-medullary, 5 (NMTC5) [MIM:616535]: A form of non-medullary thyroid cancer (NMTC), a cancer characterized by tumors originating from the thyroid follicular cells. NMTCs represent approximately 95% of all cases of thyroid cancer and are classified into papillary, follicular, Hurthle cell, and anaplastic neoplasms. {ECO:0000269|PubMed:12578864, ECO:0000269|PubMed:26222560}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.123
• rvis_EVS: -0.06
• rvis_percentile_EVS: 48.89

Haploinsufficiency Scores

• pHI: 0.454
• hipred: N
• hipred_score: 0.180
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0875

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Habp2
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: proteolysis;cell adhesion
• Cellular component: extracellular region;extracellular space
• Molecular function: serine-type endopeptidase activity;calcium ion binding;glycosaminoglycan binding