HAPLN4

hyaluronan and proteoglycan link protein 4, the group of V-set domain containing

Basic information

Region (hg38): 19:19254756-19262804

Links

ENSG00000187664 ∙ NCBI:404037 ∙ OMIM:619710 ∙ HGNC:31357 ∙ Uniprot:Q86UW8 ∙ 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 HAPLN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAPLN4 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					2	2
missense			40			40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	0	2

Variants in HAPLN4

This is a list of pathogenic ClinVar variants found in the HAPLN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19257822-C-T		not specified	Uncertain significance (Sep 04, 2024)
19-19257860-C-G		not specified	Uncertain significance (Jan 23, 2025)
19-19257870-C-T		not specified	Uncertain significance (Jun 17, 2024)
19-19257882-C-A		not specified	Uncertain significance (Feb 13, 2025)
19-19257900-C-T		not specified	Uncertain significance (Aug 26, 2022)
19-19257920-G-A		not specified	Uncertain significance (Jan 04, 2024)
19-19257951-A-C		not specified	Uncertain significance (May 30, 2024)
19-19257952-G-A			Benign (May 14, 2018)
19-19257998-C-T		not specified	Uncertain significance (Mar 01, 2024)
19-19258050-C-A		not specified	Uncertain significance (Sep 09, 2024)
19-19258071-T-G		not specified	Uncertain significance (Nov 10, 2024)
19-19258087-C-G		not specified	Uncertain significance (Feb 08, 2025)
19-19258095-T-C		not specified	Uncertain significance (Dec 27, 2022)
19-19258142-G-A		not specified	Uncertain significance (Mar 14, 2025)
19-19258142-G-T		not specified	Uncertain significance (Jan 23, 2023)
19-19258157-G-T		not specified	Uncertain significance (Mar 30, 2024)
19-19258181-C-T		not specified	Uncertain significance (Sep 27, 2021)
19-19258565-C-T		not specified	Uncertain significance (Nov 09, 2024)
19-19258628-T-C		not specified	Uncertain significance (Jul 12, 2023)
19-19258639-C-A		not specified	Uncertain significance (Oct 26, 2022)
19-19258660-C-T		not specified	Uncertain significance (Dec 11, 2024)
19-19258667-G-A		not specified	Uncertain significance (Jun 24, 2022)
19-19258680-T-C			Benign (May 14, 2018)
19-19258694-C-T		not specified	Uncertain significance (Sep 17, 2021)
19-19258709-C-G		not specified	Uncertain significance (Jan 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HAPLN4	protein_coding	protein_coding	ENST00000291481	5	7156

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0108	0.981	125577	0	36	125613	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	192	273	0.704	0.0000203	2454
Missense in Polyphen		88	116.03	0.75842		1020
Synonymous	1.91	103	131	0.787	0.0000107	899
Loss of Function	2.31	6	15.9	0.376	9.46e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000958	0.0000910
Ashkenazi Jewish	0.00148	0.00139
East Asian	0.000505	0.000490
Finnish	0.0000572	0.0000462
European (Non-Finnish)	0.0000329	0.0000264
Middle Eastern	0.000505	0.000490
South Asian	0.000165	0.000163
Other	0.000355	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to hyaluronic acid and may be involved in formation of the extracellular matrix. {ECO:0000250|UniProtKB:Q80WM4}.

Recessive Scores

• pRec: 0.114

Haploinsufficiency Scores

• pHI: 0.167
• hipred: Y
• hipred_score: 0.670
• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.235

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hapln4
• 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)

Gene ontology

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