SPTSSB

Chr 3

serine palmitoyltransferase small subunit B

Also known as: ADMP, C3orf57, SSSPTB

NCBI Gene: 165679 ENSG00000196542 UniProt: Q8NFR3

Serine palmitoyltransferase (SPT; EC 2.3.1.50) catalyzes the first committed and rate-limiting step in sphingolipid biosynthesis. SSSPTB is a small SPT subunit that stimulates SPT activity and confers acyl-CoA preference to the SPT catalytic heterodimer of SPTLC1 (MIM 605712) and either SPTLC2 (MIM 605713) or SPTLC3 (MIM 611120) (Han et al., 2009 [PubMed 19416851]).[supplied by OMIM, Nov 2010]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.91

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.91LOEUF

pLI 0.001

Z-score -0.47

OE 1.29 (0.58–1.91)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.12Z-score

OE missense 0.95 (0.74–1.23)

41 obs / 43.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.29 (0.58–1.91)

0≤0.351.4

Missense OE?0.95 (0.74–1.23)

0≤0.61.4

Synonymous OE?1.05

0≤1.21.6

LoF obs/exp: 4 / 3.1Missense obs/exp: 41 / 43.2Syn Z: -0.15

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

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 990

98 rare PASS variants

Rare truncating (LoF)

1 in 16,000

14 rare PASS variants

Rare synonymous (reference)

1 in 3,100

30 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SPTSSB. 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)	~556k	1 in 1,600	1 in 16,000
South Asian	~43k	1 in 660	≈ 1 in 43,000
Remaining (unassigned)	~30k	1 in 610	≈ 1 in 29,000
European (Finnish)	~27k	1 in 1,800	none seen
Admixed American	~22k	1 in 380	≈ 1 in 11,000
African / African American	~21k	1 in 610	≈ 1 in 6,000
East Asian	~20k	1 in 2,800	≈ 1 in 9,900
Middle Eastern	~2,884	1 in 480	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 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓