HAPLN2

hyaluronan and proteoglycan link protein 2, the group of V-set domain containing

Basic information

Region (hg38): 1:156619331-156625725

Links

ENSG00000132702 ∙ NCBI:60484 ∙ OMIM:619726 ∙ HGNC:17410 ∙ Uniprot:Q9GZV7 ∙ 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 HAPLN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAPLN2 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			17		1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	2

Variants in HAPLN2

This is a list of pathogenic ClinVar variants found in the HAPLN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156623497-G-A		not specified	Uncertain significance (Mar 28, 2024)
1-156623506-A-G		not specified	Uncertain significance (Jan 07, 2022)
1-156623562-C-T			Benign (Jun 26, 2018)
1-156623915-G-C		not specified	Uncertain significance (Jun 07, 2024)
1-156623941-G-C		not specified	Uncertain significance (Apr 09, 2024)
1-156623996-G-A		not specified	Uncertain significance (Apr 04, 2023)
1-156624007-C-T		not specified	Uncertain significance (Nov 19, 2022)
1-156624073-G-T		not specified	Uncertain significance (Mar 25, 2024)
1-156624087-C-A		not specified	Uncertain significance (May 29, 2024)
1-156624121-A-C		not specified	Uncertain significance (Feb 03, 2022)
1-156624121-A-G		not specified	Uncertain significance (Dec 20, 2023)
1-156624123-C-G		not specified	Uncertain significance (Feb 03, 2022)
1-156624136-G-T			Benign (Nov 20, 2018)
1-156624658-G-C		not specified	Uncertain significance (Apr 08, 2024)
1-156624664-C-T		not specified	Uncertain significance (Mar 20, 2024)
1-156624693-G-T		not specified	Uncertain significance (Mar 03, 2022)
1-156624697-G-A		not specified	Uncertain significance (May 23, 2024)
1-156624729-C-T		not specified	Uncertain significance (Apr 18, 2023)
1-156624736-G-C		not specified	Uncertain significance (Dec 08, 2023)
1-156625106-G-C		not specified	Uncertain significance (Nov 18, 2023)
1-156625131-C-G		not specified	Uncertain significance (May 18, 2022)
1-156625190-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-156625235-G-T		not specified	Uncertain significance (Jan 19, 2022)
1-156625247-G-A		not specified	Uncertain significance (Oct 27, 2022)
1-156625286-C-G		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HAPLN2	protein_coding	protein_coding	ENST00000255039	5	6432

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.12e-7	0.486	125402	0	18	125420	0.0000718

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	142	193	0.735	0.00000918	2104
Missense in Polyphen		58	84.34	0.68769		941
Synonymous	1.92	62	84.4	0.734	0.00000413	722
Loss of Function	0.773	11	14.1	0.778	6.15e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000218	0.000211
Ashkenazi Jewish	0.000105	0.0000995
East Asian	0.000111	0.000109
Finnish	0.0000466	0.0000463
European (Non-Finnish)	0.0000562	0.0000529
Middle Eastern	0.000111	0.000109
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates a firm binding of versican V2 to hyaluronic acid. May play a pivotal role in the formation of the hyaluronan- associated matrix in the central nervous system (CNS) which facilitates neuronal conduction and general structural stabilization. Binds to hyaluronic acid (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.108

Haploinsufficiency Scores

• pHI: 0.469
• hipred: Y
• hipred_score: 0.526
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.327

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hapln2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: skeletal system development;cell adhesion;central nervous system development;establishment of blood-nerve barrier;extracellular matrix assembly
• Cellular component: extracellular matrix
• Molecular function: hyaluronic acid binding