FAM107A
family with sequence similarity 107 member A
Basic information
Region (hg38): 3:58564117-58627610
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM107A gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 16 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 0 | 1 |
Variants in FAM107A
This is a list of pathogenic ClinVar variants found in the FAM107A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-58566606-G-C | not specified | Uncertain significance (Jan 02, 2024) | ||
| 3-58566607-C-A | not specified | Uncertain significance (Sep 22, 2023) | ||
| 3-58566608-T-C | not specified | Uncertain significance (Aug 04, 2021) | ||
| 3-58566610-G-T | not specified | Uncertain significance (Jun 09, 2022) | ||
| 3-58566658-G-C | not specified | Uncertain significance (Feb 27, 2023) | ||
| 3-58566661-G-A | not specified | Uncertain significance (Dec 05, 2022) | ||
| 3-58567228-G-A | not specified | Uncertain significance (Oct 03, 2022) | ||
| 3-58567263-C-T | not specified | Uncertain significance (Jan 31, 2022) | ||
| 3-58567326-A-T | not specified | Uncertain significance (Nov 10, 2022) | ||
| 3-58569715-C-T | not specified | Uncertain significance (Sep 06, 2022) | ||
| 3-58569736-C-T | not specified | Uncertain significance (Jan 03, 2024) | ||
| 3-58569740-A-G | not specified | Uncertain significance (Nov 17, 2022) | ||
| 3-58569794-C-G | not specified | Uncertain significance (Feb 17, 2022) | ||
| 3-58569801-T-C | Benign (Jul 16, 2018) | |||
| 3-58569814-A-C | not specified | Uncertain significance (Sep 29, 2023) | ||
| 3-58569826-A-G | not specified | Uncertain significance (Dec 06, 2022) | ||
| 3-58569835-C-T | not specified | Uncertain significance (Jul 14, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FAM107A | protein_coding | protein_coding | ENST00000394481 | 3 | 63494 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 8.28e-7 | 0.0937 | 125735 | 0 | 13 | 125748 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0978 | 90 | 92.6 | 0.971 | 0.00000628 | 925 |
| Missense in Polyphen | 38 | 43.325 | 0.87709 | 413 | ||
| Synonymous | -0.180 | 38 | 36.6 | 1.04 | 0.00000211 | 284 |
| Loss of Function | -0.887 | 8 | 5.71 | 1.40 | 2.41e-7 | 71 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000878 | 0.0000878 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000532 | 0.0000527 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000999 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Stress-inducible actin-binding protein that plays a role in synaptic and cognitive functions by modulating actin filamentous (F-actin) dynamics. Mediates polymerization of globular actin to F-actin. Also binds to, stabilizes and bundles F-actin. Involved in synaptic function by regulating neurite outgrowth in an actin-dependent manner and for the acquisition of hippocampus-dependent cognitive function, such as learning and long-term memory (By similarity). Plays a role in the actin and microtubule cytoskeleton organization; negatively regulates focal adhesion (FA) assembly promoting malignant glial cell migration in an actin-, microtubule- and MAP1A-dependent manner (PubMed:20543869). Also involved in neuroblastoma G1/S phase cell cycle progression and cell proliferation inhibition by stimulating ubiquitination of NF-kappa-B subunit RELA and NF-kappa-B degradation in a COMMD1- and actin-dependent manner (PubMed:10564580, PubMed:28604741). May play a role in tumor development (PubMed:10564580). {ECO:0000250|UniProtKB:Q78TU8, ECO:0000269|PubMed:10564580, ECO:0000269|PubMed:20543869, ECO:0000269|PubMed:28604741}.;
Recessive Scores
- pRec
- 0.140
Intolerance Scores
- loftool
- 0.759
- rvis_EVS
- 0.48
- rvis_percentile_EVS
- 79.04
Haploinsufficiency Scores
- pHI
- 0.166
- hipred
- Y
- hipred_score
- 0.506
- ghis
- 0.412
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.855
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fam107a
- Phenotype
Gene ontology
- Biological process
- regulation of cell growth;cell cycle;actin filament polymerization;positive regulation of cell migration;positive regulation of protein ubiquitination;regulation of protein stability;cellular response to nutrient levels;regulation of actin cytoskeleton organization;cognition;actin filament bundle assembly;negative regulation of focal adhesion assembly;regulation of microtubule cytoskeleton organization;cellular response to glucocorticoid stimulus;negative regulation of long-term synaptic potentiation;negative regulation of G1/S transition of mitotic cell cycle
- Cellular component
- stress fiber;nucleus;cytoplasm;focal adhesion;actin cytoskeleton;nuclear speck;ruffle membrane;neuron projection;synapse
- Molecular function
- molecular_function;actin binding;protein binding