HAPLN3

protein-coding

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

Gene summary

This gene belongs to the hyaluronan and proteoglycan binding link protein gene family. The protein encoded by this gene may function in hyaluronic acid binding and cell adhesion. [provided by RefSeq, Jul 2008]

Previous symbols:

EXLD1

MANE transcript

NM_178232.4

Inheritance

—

ClinVar variants

U:107B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr15:88,877,294-88,895,597

External References & Databases

Ensembl (ENSG00000140511)

Transcript & Mutation Effects

hg38 • Region Span ~18.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HAPLN3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 101

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178232.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			105 clinvar	4 clinvar		109
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	107	4	0	111

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178232.4	RefSeq	NP_839946.1	4	MANE Select
ENST00000359595.8	Ensembl	ENSP00000352606.4	4	MANE Select
NM_001307952.2	RefSeq	NP_001294881.1	5	Standard
ENST00000558770.5	Ensembl	ENSP00000456458.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

skeletal system development
cell adhesion
central nervous system development

Molecular Function

hyaluronic acid binding

Cellular Component

extracellular space
extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359595
Coding exons: 4
Length: 18339
Individuals with no LoFs: 125684
Homozygous LoFs: 0
Heterozygous LoFs: 64
Defined: 125748
p: 0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.222	243	253	0.961	0.0000182	2300
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00033	0.00031	rare
Latino/Admixed American	0.00036	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00065	0.00065	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.000097	rare
South Asian	0.00056	0.00056	rare
Other	0.0012	0.0011	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.361

Gene Damage Prediction

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