FAM107A

family with sequence similarity 107 member A

Basic information

Region (hg38): 3:58564117-58627610

Links

ENSG00000168309

∙ NCBI:11170 ∙ OMIM:608295 ∙ HGNC:30827 ∙ Uniprot:O95990 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM107A gene.

not_specified (24 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_001076778.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			23 clinvar			23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	1	1

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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