HAPLN1
Basic information
Region (hg38): 5:83637805-83720855
Previous symbols: [ "CRTL1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (39 variants)
- not_provided (1 variants)
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. These statistics are base on transcript: NM_000001884.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 38 | 39 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 38 | 2 | 0 |
GnomAD
Source:
| 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:
- 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