FAM20B

protein-coding

FAM20B glycosaminoglycan xylosylkinase, the group of Golgi associated kinase family

Gene summary

Enables phosphotransferase activity, alcohol group as acceptor. Predicted to be involved in proteoglycan biosynthetic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014864.4

Inheritance

ClinVar variants

P:1U:59B:1

Top phenotype

Desbuquois syndrome

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr1:179,025,804-179,076,567

External References & Databases

Ensembl (ENSG00000116199)

Transcript & Mutation Effects

hg38 • Region Span ~50.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

congenital disorder of glycosylationLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0015286

Submitter: ClinGen

*FAM20B* was first reported in relation to autosomal recessive congenital disorder of glycosylation in 2019 (Kuroda et al., PMID: 33798445). Two unique frameshift variants that have been reported in one proband in one publication are included in this curation. This gene-disease relationship is also supported by a biochemical function study (Koike et al, PMID: 19473117) and multiple animal models (PMIDs: 21901110, 27405802, 3015814). After discussion with the expert panel, although the point total is consistent with Moderate, since only one clinical case has been reported, this gene-disease relationship has been downgraded to Limited. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the ClinGen Congenital Disorders of Glycosylation GCEP on the meeting date April 3, 2025 (SOP Version 11).

Desbuquois dysplasiaMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0015426

Submitter: PanelApp Australia

Desbuquois dysplasiaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0015426

Submitter: Franklin by Genoox

Two affected boy and girl who had mid-face hypoplasia, thoracic hypoplasia, very short stature with mesomelic shortening of the limbs, and multiple dislocations of the large joints. Molecular analyses of the girl showed compound heterozygous variants in FAM20B. https://doi.org/10.1111/cge.13530

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAM20B variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 52

Desbuquois syndromeTotal: 2

not providedTotal: 1

FAM20B-related disorderTotal: 1

FAM20B-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014864.4. 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 clinvar		2
missense			53 clinvar			53
nonsense						0
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	1	59	1	0	61

Highest pathogenic variant AF is 6.8661416e-7

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014864.4	RefSeq	NP_055679.1	7	MANE Select
ENST00000263733.5	Ensembl	ENSP00000263733.4	7	MANE Select
NM_001324310.2	RefSeq	NP_001311239.1	7	Standard
NM_001324311.2	RefSeq	NP_001311240.1	7	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
fam20b	Danio rerio	Structure: perichondral bone Quality: hyperplastic abnormal

Gene / Model

Organism

Observed Phenotype

fam20b

Danio rerio

Structure: perichondral bone

Quality: hyperplastic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Immune System
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Adaptive Immune System
Endosomal/Vacuolar pathway
Antigen processing-Cross presentation

Biological Process

protein phosphorylation
proteoglycan biosynthetic process

Molecular Function

protein binding
ATP binding
kinase activity
phosphotransferase activity, alcohol group as acceptor
metal ion binding

Cellular Component

Golgi membrane
nucleoplasm
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000263733
Coding exons: 7
Length: 50759
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125748
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.979	196	239	0.822	0.0000132	2672
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000089	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000067	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.262
RVIS EVS: -0.12
RVIS percentile EVS: 45.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.136

Gene Damage Prediction

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