FAM20B

Chr 1

FAM20B glycosaminoglycan xylosylkinase

Also known as: gxk1

NCBI Gene: 9917 ENSG00000116199 UniProt: O75063 OMIM: 611063

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]

OMIM Research

OMIM ResearchGenerating clinical summary…

Clinical highlights

Gene–disease validity (ClinGen)

Limited · congenital disorder of glycosylation · AR · ClinGen 2025

not for standalone diagnostic reporting

Active trials

—

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.91

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.91LOEUF

pLI 0.000

Z-score 1.86

OE 0.56 (0.36–0.91)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.98Z-score

OE missense 0.82 (0.73–0.93)

196 obs / 238.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.56 (0.36–0.91)

0≤0.351.4

Missense OE?0.82 (0.73–0.93)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 12 / 21.3Missense obs/exp: 196 / 238.6Syn Z: 0.16

Background carrier burden — how many people carry a rare variant somewhere in FAM20B?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 160

467 rare PASS variants

Rare truncating (LoF)

1 in 4,400

53 rare PASS variants

Rare synonymous (reference)

1 in 360

193 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for FAM20B. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 190	1 in 4,000
South Asian	~43k	1 in 170	1 in 5,400
Remaining (unassigned)	~30k	1 in 150	≈ 1 in 7,500
European (Finnish)	~27k	1 in 260	1 in 2,400
Admixed American	~22k	1 in 150	≈ 1 in 5,500
African / African American	~21k	1 in 110	1 in 3,500
East Asian	~20k	1 in 230	≈ 1 in 6,600
Ashkenazi Jewish	~13k	1 in 620	≈ 1 in 4,400
Middle Eastern	~2,884	1 in 130	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 6 of 7 coding exons well covered in gnomAD exomes; exon 4 marginal. Genomes: all 7.? see exons ↓