HAPLN1

hyaluronan and proteoglycan link protein 1, the group of V-set domain containing

Basic information

Region (hg38): 5:83637805-83720855

Previous symbols: [ "CRTL1" ]

Links

ENSG00000145681 ∙ NCBI:1404 ∙ OMIM:115435 ∙ HGNC:2380 ∙ Uniprot:P10915 ∙ 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 HAPLN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAPLN1 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
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in HAPLN1

This is a list of pathogenic ClinVar variants found in the HAPLN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-83641554-C-G		not specified	Uncertain significance (May 21, 2024)
5-83641563-C-G		not specified	Uncertain significance (Jun 01, 2023)
5-83641579-T-C		not specified	Uncertain significance (Jun 03, 2022)
5-83641742-A-C		not specified	Uncertain significance (Apr 17, 2023)
5-83641758-G-A		not specified	Uncertain significance (Feb 28, 2023)
5-83644413-T-G		not specified	Uncertain significance (Mar 25, 2024)
5-83644444-C-T		not specified	Uncertain significance (Oct 20, 2024)
5-83644550-G-A			Likely benign (Apr 01, 2022)
5-83644566-A-G		not specified	Uncertain significance (Aug 17, 2021)
5-83644582-C-A		not specified	Uncertain significance (May 13, 2024)
5-83644586-C-G		not specified	Uncertain significance (Dec 10, 2024)
5-83644632-C-A		not specified	Uncertain significance (Dec 13, 2022)
5-83644633-G-A		not specified	Uncertain significance (Mar 15, 2024)
5-83644645-G-C		not specified	Uncertain significance (Sep 10, 2024)
5-83652474-C-T		not specified	Uncertain significance (Oct 12, 2022)
5-83652584-A-G		not specified	Uncertain significance (Oct 29, 2024)
5-83652606-C-T		not specified	Uncertain significance (Aug 01, 2022)
5-83652722-G-A		not specified	Uncertain significance (Nov 21, 2024)
5-83652755-A-G		not specified	Uncertain significance (Jun 08, 2022)
5-83652759-T-G		not specified	Uncertain significance (Mar 30, 2024)
5-83673439-C-T		not specified	Uncertain significance (Jan 16, 2024)
5-83673454-G-T		not specified	Uncertain significance (Feb 15, 2023)
5-83673462-T-C		not specified	Uncertain significance (Aug 02, 2022)
5-83673490-T-C		not specified	Likely benign (Aug 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HAPLN1	protein_coding	protein_coding	ENST00000274341	4	83809

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.602	0.397	125729	0	7	125736	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.414	182	198	0.917	0.0000112	2294
Missense in Polyphen		63	85.288	0.73867		857
Synonymous	-1.06	90	78.1	1.15	0.00000454	692
Loss of Function	3.00	3	15.9	0.189	9.02e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000549	0.0000544
South Asian	0.00	0.00
Other	0.000190	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stabilizes the aggregates of proteoglycan monomers with hyaluronic acid in the extracellular cartilage matrix.
• Pathway: Extracellular matrix organization;ECM proteoglycans (Consensus)

Recessive Scores

• pRec: 0.185

Intolerance Scores

• loftool: 0.341
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.218
• hipred: Y
• hipred_score: 0.699
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.946

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hapln1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic 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); limbs/digits/tail phenotype; hearing/vestibular/ear phenotype; skeleton phenotype; growth/size/body region phenotype; craniofacial phenotype

Zebrafish Information Network

• Gene name: hapln1b
• Affected structure: dorsal longitudinal anastomotic vessel
• Phenotype tag: abnormal
• Phenotype quality: hypoplastic

Gene ontology

• Biological process: skeletal system development;cell adhesion;central nervous system development;extracellular matrix organization
• Cellular component: extracellular region;extracellular matrix;synapse;collagen-containing extracellular matrix
• Molecular function: hyaluronic acid binding;extracellular matrix structural constituent conferring compression resistance