HAPLN3

hyaluronan and proteoglycan link protein 3, the group of V-set domain containing

Basic information

Region (hg38): 15:88877294-88895597

Previous symbols: [ "EXLD1" ]

Links

ENSG00000140511 ∙ NCBI:145864 ∙ ∙ HGNC:21446 ∙ Uniprot:Q96S86 ∙ 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 HAPLN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAPLN3 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			55	4		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	4	0

Variants in HAPLN3

This is a list of pathogenic ClinVar variants found in the HAPLN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-88877996-C-T		not specified	Uncertain significance (May 04, 2023)
15-88877998-T-C		not specified	Uncertain significance (Oct 08, 2024)
15-88878000-C-G		not specified	Uncertain significance (Aug 02, 2022)
15-88878004-C-T		not specified	Uncertain significance (Feb 10, 2025)
15-88878017-C-T		not specified	Uncertain significance (Aug 23, 2021)
15-88878056-C-A		not specified	Uncertain significance (Jan 19, 2025)
15-88878089-G-A		not specified	Uncertain significance (Oct 22, 2021)
15-88878092-C-T		not specified	Uncertain significance (Dec 05, 2022)
15-88878149-C-A		not specified	Uncertain significance (Sep 14, 2023)
15-88878178-G-A		not specified	Uncertain significance (Oct 12, 2021)
15-88878187-T-C		not specified	Uncertain significance (Feb 21, 2024)
15-88878233-G-C		not specified	Uncertain significance (Dec 19, 2023)
15-88878972-A-G		not specified	Uncertain significance (Jan 09, 2024)
15-88879003-G-A		not specified	Uncertain significance (Jan 26, 2025)
15-88879006-G-A		not specified	Uncertain significance (Jul 05, 2023)
15-88879021-G-A		not specified	Uncertain significance (May 18, 2023)
15-88879023-G-A		not specified	Uncertain significance (Oct 20, 2024)
15-88879039-C-A		not specified	Uncertain significance (Dec 15, 2024)
15-88879056-G-A		not specified	Likely benign (Jun 21, 2023)
15-88879057-G-A		not specified	Uncertain significance (Jul 06, 2024)
15-88879083-A-G		not specified	Likely benign (Jul 25, 2023)
15-88879090-G-A		not specified	Uncertain significance (Mar 02, 2023)
15-88879122-G-A		not specified	Uncertain significance (Jan 20, 2025)
15-88879123-C-T		not specified	Uncertain significance (Feb 28, 2023)
15-88879129-A-G		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HAPLN3	protein_coding	protein_coding	ENST00000359595	4	18339

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000101	0.559	125684	0	64	125748	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.222	243	253	0.961	0.0000182	2300
Missense in Polyphen		111	114.43	0.97005		1007
Synonymous	-0.0837	110	109	1.01	0.00000776	752
Loss of Function	0.891	11	14.7	0.749	7.05e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000686	0.000663
Ashkenazi Jewish	0.00	0.00
East Asian	0.000652	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000109	0.0000967
Middle Eastern	0.000652	0.000653
South Asian	0.000558	0.000555
Other	0.00116	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in hyaluronic acid binding. {ECO:0000303|PubMed:12663660}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.822
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.43

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.251
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.361

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hapln3

Gene ontology

• Biological process: skeletal system development;cell adhesion;central nervous system development
• Cellular component: extracellular space;extracellular matrix
• Molecular function: hyaluronic acid binding