S100G

Chr X

S100 calcium binding protein G

Also known as: CABP, CABP1, CABP9K, CALB3

NCBI Gene: 795 ENSG00000169906 UniProt: P29377 OMIM: 302020

Calbindin D9K is a vitamin D-dependent calcium-binding protein that buffers cytoplasmic calcium and facilitates ATP-dependent calcium transport, particularly in intestinal absorption. Mutations in S100G cause autosomal recessive congenital cataracts, facial dysmorphism, and neuropathy (CCFDN), a disorder affecting the eyes, nervous system, and facial development. This gene is not highly constrained against loss-of-function variants, and the condition follows autosomal recessive inheritance.

OMIM ResearchSummary from RefSeq

This gene encodes calbindin D9K, a vitamin D-dependent calcium-binding protein. This cytosolic protein belongs to a family of calcium-binding proteins that includes calmodulin, parvalbumin, troponin C, and S100 protein. In the intestine, the protein is vitamin D-dependent and its expression correlates with calcium transport activity. The protein may increase Ca2+ absorption by buffering Ca2+ in the cytoplasm and increase ATP-dependent Ca2+ transport in duodenal basolateral membrane vesicles. [provided by RefSeq, Jul 2008]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.84

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.84LOEUF

pLI 0.115

Z-score 0.35

OE 0.69 (0.21–1.84)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.38Z-score

OE missense 0.78 (0.54–1.15)

18 obs / 23.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.69 (0.21–1.84)

0≤0.351.4

Missense OE?0.78 (0.54–1.15)

0≤0.61.4

Synonymous OE?0.85

0≤1.21.6

LoF obs/exp: 1 / 1.5Missense obs/exp: 18 / 23.1Syn Z: 0.37

Background carrier burden — how many people carry a rare variant somewhere in S100G?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 2,400

51 rare PASS variants

Rare truncating (LoF)

1 in 16,000

9 rare PASS variants

Rare synonymous (reference)

1 in 5,500

26 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for S100G. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 8 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~561k	1 in 3,400	1 in 2,400
South Asian	~36k	1 in 1,200	1 in 690
Remaining (unassigned)	~31k	1 in 780	≈ 1 in 29,000
European (Finnish)	~27k	1 in 2,000	≈ 1 in 13,000
Admixed American	~23k	1 in 3,900	≈ 1 in 23,000
African / African American	~20k	1 in 360	none seen
East Asian	~20k	1 in 1,700	≈ 1 in 20,000
Middle Eastern	~2,755	≈ 1 in 2,700	none seen

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): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓