SAMD13

Chr 1

sterile alpha motif domain containing 13

Also known as: DJL, HSD-41, HSD-42

NCBI Gene: 148418ENSG00000203943UniProt: Q5VXD3

The protein is a sterile alpha motif domain-containing protein involved in transcriptional regulation. Mutations cause autosomal recessive developmental and epileptic encephalopathy with severe intellectual disability, seizures, and developmental delay typically manifesting in infancy. The gene shows low constraint against loss-of-function variants, consistent with its recessive inheritance pattern.

Research Assistant →
0
Active trials
1
Pubs (1 yr)
16
P/LP submissions
0%
P/LP missense
1.42
LOEUF
GOF
Mechanism· predicted
Clinical Summary— SAMD13
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
16 unique Pathogenic / Likely Pathogenic· 19 VUS of 42 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.42LOEUF
pLI 0.006
Z-score 0.87
OE 0.63 (0.31–1.42)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.86Z-score
OE missense 0.69 (0.54–0.89)
42 obs / 60.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.63 (0.31–1.42)
0≤0.351.4
Missense OE0.69 (0.54–0.89)
0≤0.61.4
Synonymous OE0.97
0≤1.21.6
LoF obs/exp: 4 / 6.4Missense obs/exp: 42 / 60.9Syn Z: 0.12
DN
0.6064th %ile
GOF
0.73top 25%
LOF
0.3648th %ile

The highest-scoring mechanism for this gene is gain-of-function.

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

42 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic14
Likely Pathogenic2
VUS19
14
Pathogenic
2
Likely Pathogenic
19
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
14
0
14
Likely Pathogenic
0
0
2
0
2
VUS
0
15
4
0
19
Likely Benign
0
0
0
0
0
Benign
0
0
0
0
0
Total01520035

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

View in ClinVar →

Protein Context — Lollipop Plot

SAMD13 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

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