HABP4

hyaluronan binding protein 4

Basic information

Region (hg38): 9:96450168-96491336

Links

ENSG00000130956 ∙ NCBI:22927 ∙ OMIM:617369 ∙ HGNC:17062 ∙ Uniprot:Q5JVS0 ∙ 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 HABP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HABP4 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			24	2		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in HABP4

This is a list of pathogenic ClinVar variants found in the HABP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-96450376-G-T		not specified	Uncertain significance (Oct 20, 2023)
9-96450533-C-T		not specified	Uncertain significance (Oct 17, 2023)
9-96450578-C-A		not specified	Uncertain significance (May 17, 2023)
9-96458391-C-T		not specified	Uncertain significance (Dec 21, 2022)
9-96458414-G-A		not specified	Uncertain significance (Aug 12, 2021)
9-96458460-A-C		not specified	Uncertain significance (Mar 20, 2024)
9-96458462-C-T		not specified	Uncertain significance (Oct 31, 2023)
9-96458524-G-T		not specified	Uncertain significance (Apr 24, 2024)
9-96465339-C-T		not specified	Uncertain significance (Nov 29, 2023)
9-96465387-C-T		not specified	Uncertain significance (Feb 13, 2024)
9-96465396-G-T		not specified	Uncertain significance (Jul 20, 2021)
9-96465404-G-A		not specified	Likely benign (Sep 16, 2021)
9-96465443-G-A		not specified	Uncertain significance (Apr 12, 2024)
9-96465494-A-G		not specified	Uncertain significance (Oct 03, 2022)
9-96465728-C-A		not specified	Uncertain significance (Mar 23, 2023)
9-96465733-T-C		not specified	Uncertain significance (Dec 17, 2023)
9-96465760-G-A		not specified	Uncertain significance (Feb 15, 2023)
9-96465763-C-T		not specified	Uncertain significance (Mar 29, 2022)
9-96471031-C-T		not specified	Likely benign (Oct 06, 2021)
9-96471058-A-C		not specified	Uncertain significance (Mar 22, 2023)
9-96471066-G-A		not specified	Uncertain significance (Jan 26, 2022)
9-96484553-C-A		not specified	Uncertain significance (Nov 02, 2023)
9-96488102-A-C		not specified	Uncertain significance (Aug 23, 2021)
9-96488105-A-G		not specified	Uncertain significance (Dec 16, 2023)
9-96488113-G-A		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HABP4	protein_coding	protein_coding	ENST00000375249	8	41136

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00621	0.990	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	168	214	0.784	0.0000127	2657
Missense in Polyphen		40	58.508	0.68367		654
Synonymous	1.30	63	77.6	0.812	0.00000451	830
Loss of Function	2.53	7	18.9	0.371	0.00000110	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.000816	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.0000704	0.0000703
Middle Eastern	0.000816	0.000816
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that plays a role in the regulation of transcription, pre-mRNA splicing and mRNA translation (PubMed:14699138, PubMed:16455055, PubMed:19523114, PubMed:21771594). Negatively regulates DNA-binding activity of the transcription factor MEF2C in myocardial cells in response to mechanical stress (By similarity). Plays a role in pre-mRNA splicing regulation (PubMed:19523114). Binds (via C-terminus) to poly(U) RNA (PubMed:19523114). Involved in mRNA translation regulation, probably at the initiation step (PubMed:21771594). {ECO:0000250|UniProtKB:A1L1K8, ECO:0000269|PubMed:14699138, ECO:0000269|PubMed:16455055, ECO:0000269|PubMed:19523114, ECO:0000269|PubMed:21771594}.
• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.593
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.184
• hipred: Y
• hipred_score: 0.573
• ghis: 0.628

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.759

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Habp4

Gene ontology

• Biological process: platelet degranulation;mRNA processing;RNA splicing;positive regulation of RNA splicing;negative regulation of DNA binding;positive regulation of translational initiation;cellular response to mechanical stimulus
• Cellular component: extracellular region;nucleus;nucleolus;cytoplasm;cytosol;cytoplasmic stress granule;Cajal body;sarcoplasm;nuclear speck;sarcomere;Gemini of coiled bodies
• Molecular function: RNA binding;protein binding