FAM209A
protein-codingfamily with sequence similarity 209 member A
Gene summary
Predicted to be involved in cell differentiation and spermatogenesis. Located in extracellular exosome and nucleus. [provided by Alliance of Genome Resources, Jul 2025]
- C20orf106
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to FAM209A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001012971.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 22 | 3 | 25 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 23 | 3 | 0 | 26 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001012989.2 | 2 | MANE Select | |
| Ensembl | ENSP00000360379.4 | 2 | MANE Select | |
| Ensembl | ENSP00000771660.1 | 2 | Standard | |
| Ensembl | ENSP00000809855.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- biological_process
Molecular Function
- molecular_function
Cellular Component
- nucleus
- integral component of membrane
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371328
- Coding exons
- 2
- Length
- 8956
- Individuals with no LoFs
- 125183
- Homozygous LoFs
- 8
- Heterozygous LoFs
- 556
- Defined
- 125747
- p
- 0.00225
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.345 | 107 | 97.4 | 1.10 | 0.00000564 | 1116 |
| Missense (PolyPhen) | 39 | 38.459 | 1.0141 | 499 | ||
| Synonymous | 0.900 | 31 | 38.1 | 0.814 | 0.00000232 | 329 |
| Loss of Function | 1.03 | 2 | 4.29 | 0.466 | 1.88e-7 | 40 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0023 | 0.0012 | notable |
| Latino/Admixed American | 0.0048 | 0.0024 | notable |
| Ashkenazi Jewish | 0.0012 | 0.00060 | notable |
| East Asian | 0.00071 | 0.00038 | rare |
| Finnish | 0.00088 | 0.00046 | rare |
| European (Non-Finnish) | 0.0060 | 0.0030 | notable |
| South Asian | 0.0043 | 0.0022 | notable |
| Other | 0.011 | 0.0057 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- 0.42
- RVIS percentile EVS
- 76.81
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |