CASD1

Chr 7

CAS1 domain sialic acid O acetyltransferase 1

Also known as: C7orf12, Cas1, Cas1p, NBLA04196, SOAT

NCBI Gene: 64921ENSG00000127995UniProt: Q96PB1

Enables N-acetylneuraminate 9-O-acetyltransferase activity. Involved in carbohydrate metabolic process. Located in Golgi membrane. [provided by Alliance of Genome Resources, Jul 2025]

567
ClinVar variants
115
Pathogenic / LP
0.04
pLI score
0
Active trials
Clinical Summary— CASD1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.26) despite low pLI — interpret in context.
📋
ClinVar Variants
115 Pathogenic / Likely Pathogenic· 305 VUS of 567 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.43LOEUF
pLI 0.045
Z-score 4.42
OE 0.26 (0.16–0.43)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.96Z-score
OE missense 0.73 (0.66–0.80)
294 obs / 405.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.26 (0.16–0.43)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.73 (0.66–0.80)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.98
0≤1.21.6
LoF obs/exp: 11 / 41.9Missense obs/exp: 294 / 405.3Syn Z: 0.21

ClinVar Variant Classifications

567 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic84
Likely Pathogenic31
VUS305
Likely Benign123
Benign11
Conflicting13
84
Pathogenic
31
Likely Pathogenic
305
VUS
123
Likely Benign
11
Benign
13
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
49
1
34
0
84
Likely Pathogenic
14
7
10
0
31
VUS
5
272
24
4
305
Likely Benign
0
4
56
63
123
Benign
0
3
6
2
11
Conflicting
—13
Total6828713069567

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CASD1 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools