FAM20B
FAM20B glycosaminoglycan xylosylkinase, the group of Golgi associated kinase family
Basic information
Region (hg38): 1:179025804-179076567
Links
Phenotypes
GenCC
Source:
- Desbuquois dysplasia (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM20B 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 | 15 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 0 | 0 |
Variants in FAM20B
This is a list of pathogenic ClinVar variants found in the FAM20B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-179043864-G-A | not specified | Uncertain significance (Jun 25, 2024) | ||
| 1-179043948-A-G | not specified | Uncertain significance (Mar 30, 2024) | ||
| 1-179043951-G-A | not specified | Uncertain significance (Aug 04, 2021) | ||
| 1-179043965-G-A | not specified | Uncertain significance (Nov 10, 2024) | ||
| 1-179043975-G-A | not specified | Uncertain significance (Jan 22, 2024) | ||
| 1-179044034-C-T | not specified | Uncertain significance (Feb 14, 2024) | ||
| 1-179044080-C-T | not specified | Uncertain significance (Jul 11, 2023) | ||
| 1-179044112-C-T | not specified | Uncertain significance (Jul 12, 2023) | ||
| 1-179044148-G-A | not specified | Uncertain significance (Feb 14, 2023) | ||
| 1-179044186-A-G | FAM20B-related condition | Likely benign (Apr 02, 2024) | ||
| 1-179050293-A-G | not specified | Uncertain significance (Jul 25, 2023) | ||
| 1-179050311-C-A | not specified | Uncertain significance (Jul 25, 2024) | ||
| 1-179054561-T-C | not specified | Uncertain significance (Jun 08, 2022) | ||
| 1-179054573-T-C | not specified | Uncertain significance (Jan 18, 2023) | ||
| 1-179054582-G-A | not specified | Uncertain significance (Oct 28, 2024) | ||
| 1-179054628-C-G | not specified | Uncertain significance (Jun 26, 2024) | ||
| 1-179064034-G-T | not specified | Uncertain significance (Mar 14, 2023) | ||
| 1-179064369-C-T | not specified | Uncertain significance (Oct 12, 2024) | ||
| 1-179064393-G-A | not specified | Uncertain significance (Mar 28, 2024) | ||
| 1-179064396-G-C | not specified | Uncertain significance (Sep 09, 2021) | ||
| 1-179064436-A-G | not specified | Uncertain significance (Jul 26, 2022) | ||
| 1-179064468-A-G | not specified | Uncertain significance (Jun 03, 2024) | ||
| 1-179066819-G-T | not specified | Uncertain significance (Sep 04, 2024) | ||
| 1-179071927-C-T | not specified | Uncertain significance (Sep 29, 2023) | ||
| 1-179072005-C-T | not specified | Uncertain significance (Oct 24, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FAM20B | protein_coding | protein_coding | ENST00000263733 | 7 | 50759 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000389 | 0.953 | 125726 | 0 | 22 | 125748 | 0.0000875 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.979 | 196 | 239 | 0.822 | 0.0000132 | 2672 |
| Missense in Polyphen | 47 | 71.373 | 0.65851 | 810 | ||
| Synonymous | 0.156 | 89 | 90.9 | 0.979 | 0.00000480 | 824 |
| Loss of Function | 1.86 | 12 | 21.3 | 0.564 | 0.00000143 | 215 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000335 | 0.000335 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.0000709 | 0.0000703 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.0000667 | 0.0000653 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Responsible for the 2-O-phosphorylation of xylose in the glycosaminoglycan-protein linkage region of proteoglycans thereby regulating the amount of mature GAG chains. Sulfated glycosaminoglycans (GAGs), including heparan sulfate and chondroitin sulfate, are synthesized on the so-called common GAG- protein linkage region (GlcUAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1- O-Ser) of core proteins, which is formed by the stepwise addition of monosaccharide residues by the respective specific glycosyltransferases. Xylose 2-O-phosphorylation may influence the catalytic activity of B3GAT3 (GlcAT-I) which completes the precursor tetrasaccharide of GAG-protein linkage regions on which the repeating disaccharide region is synthesized. {ECO:0000269|PubMed:19473117, ECO:0000269|PubMed:24425863}.;
- Pathway
- Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Endosomal/Vacuolar pathway;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Antigen Presentation: Folding, assembly and peptide loading of class I MHC
(Consensus)
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- loftool
- 0.262
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 45.13
Haploinsufficiency Scores
- pHI
- 0.441
- hipred
- Y
- hipred_score
- 0.543
- ghis
- 0.581
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.136
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fam20b
- Phenotype
- growth/size/body region phenotype; respiratory system phenotype; liver/biliary system phenotype; embryo 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); vision/eye phenotype; digestive/alimentary phenotype; skeleton phenotype;
Zebrafish Information Network
- Gene name
- fam20b
- Affected structure
- perichondral bone
- Phenotype tag
- abnormal
- Phenotype quality
- hyperplastic
Gene ontology
- Biological process
- protein phosphorylation;proteoglycan biosynthetic process
- Cellular component
- Golgi membrane;nucleoplasm;Golgi apparatus;integral component of membrane
- Molecular function
- protein binding;ATP binding;kinase activity;phosphotransferase activity, alcohol group as acceptor;metal ion binding