SAT1

Chr X

spermidine/spermine N1-acetyltransferase 1

Also known as: DC21, KFSD, KFSDX, SAT, SSAT, SSAT-1

NCBI Gene: 6303 ENSG00000130066 UniProt: Q9H2B4 OMIM: 313020

SAT1 encodes a sodium-independent sulfate anion transporter that also mediates exchange of other anions including bicarbonate, thiosulfate, and oxalate. Mutations cause keratosis follicularis spinulosa decalvans (KFSD), a rare skin disorder characterized by follicular hyperkeratosis and hair loss. The gene is highly constrained against loss-of-function variation (pLI 0.87, LOEUF 0.45), suggesting intolerance to haploinsufficiency.

OMIM ResearchSummary from RefSeq, UniProt

LOEUF 0.45

Clinical Summary— SAT1

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Gene-Disease Validity (ClinGen)

pediatric systemic lupus erythematosus · XLLimited

Limited evidence — not for standalone diagnostic reporting

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.87) — some intolerance to loss-of-function variants.

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ClinVar Variants

55 unique Pathogenic / Likely Pathogenic· 9 VUS of 116 total submissions

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Clinical Trials

2 active or recruiting trials — potential therapeutic options may be available

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint

0.45LOEUF

pLI 0.871

Z-score 2.40

OE 0.00 (0.00–0.45)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint

1.71Z-score

OE missense 0.40 (0.29–0.55)

25 obs / 63.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios

LoF OE0.00 (0.00–0.45)

0≤0.351.4

Missense OE0.40 (0.29–0.55)

0≤0.61.4

Synonymous OE1.57

0≤1.21.6

LoF obs/exp: 0 / 6.7Missense obs/exp: 25 / 63.1Syn Z: -2.17

ClinVar Variant Classifications

116 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic55

VUS9

Likely Benign2

Benign1

Conflicting1

Pathogenic

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	—	—	—	—	55
Likely Pathogenic	—	—	—	—	0
VUS	—	—	—	—	9
Likely Benign	—	—	—	—	2
Benign	—	—	—	—	1
Conflicting	—				1
Total	—				68

Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SAT1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

External Resources

Links to major genomics databases and tools

Franklin by Genoox

AI-powered variant curation and clinical analysis

DECIPHER

Genomic variants and phenotypes in rare disease patients

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

Gene ExpressionGene Expression ProfilingInfection

Host Response to Infection by Direct Analysis of Leukocyte Single Cell-type Gene Expression/transcript Abundance, Direct LS-TA

ACTIVE NOT RECRUITING

NCT06838780Chinese University of Hong KongStarted 2018-01-01

No intervention

Single Cell Sequencing TechnologyGene Expression ProfilingGene Expression

Host Response to Infection by Direct Analysis of Leukocyte Single Cell-type Gene Expression/transcript Abundance, Direct LS-TA. a Prospective Study Will Evaluate the Performance of Direct LS-TA in Triage Febrile Patients Into Major Categories of Infections: Viral, Bacterial or Active Tuberculosis.

NOT YET RECRUITING

NCT06846645Chinese University of Hong KongStarted 2025-02

No intervention

Clinical Literature

Open Research Assistant →

Landmark / reviewRecent case evidence

Full-Text Mentions

NLP-detected gene mentions in article bodies · via PubTator3

PubTator3

Inhibition of SAT1 alleviates chondrocyte inflammation and ferroptosis by repressing ALOX15 expression and activating the Nrf2 pathway

Xu J et al.·Bone Joint Res

2024