FAM53A
Chr 4family with sequence similarity 53 member A
Also known as: DNTNP
FAM53A is predicted to be involved in protein import into the nucleus and may play an important role in neural development, particularly in the dorsomedial roof of the third ventricle. The gene shows low constraint to loss-of-function variation (pLI 0.004, LOEUF 1.17), and no established human disease associations have been reported to date. Clinical significance of variants in this gene remains uncertain.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Tolerant to missense variation
The highest-scoring mechanism for this gene is dominant-negative.
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
278 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 137 | 0 | 137 |
Likely Pathogenic | 0 | 0 | 7 | 0 | 7 |
VUS | 0 | 88 | 15 | 0 | 103 |
Likely Benign | 0 | 10 | 2 | 2 | 14 |
Benign | 0 | 6 | 0 | 4 | 10 |
| Total | 0 | 104 | 161 | 6 | 271 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
FAM53A · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools