FAM83A

family with sequence similarity 83 member A, the group of Family with sequence similarity 83

Basic information

Region (hg38): 8:123178959-123210079

Links

ENSG00000147689 ∙ NCBI:84985 ∙ ∙ HGNC:28210 ∙ Uniprot:Q86UY5 ∙ 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 FAM83A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM83A 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						0
missense			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in FAM83A

This is a list of pathogenic ClinVar variants found in the FAM83A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-123182863-C-T		not specified	Uncertain significance (Apr 20, 2024)
8-123182894-G-A		not specified	Uncertain significance (Aug 17, 2021)
8-123182896-C-G		not specified	Uncertain significance (Jan 10, 2023)
8-123182924-G-A		not specified	Uncertain significance (Jan 23, 2024)
8-123182940-C-A		not specified	Uncertain significance (Aug 12, 2021)
8-123183024-G-C		not specified	Uncertain significance (Jun 07, 2023)
8-123183068-T-C		not specified	Uncertain significance (Apr 08, 2024)
8-123183097-C-G		not specified	Likely benign (Nov 17, 2023)
8-123183119-C-T		not specified	Uncertain significance (Jul 27, 2021)
8-123183174-C-A		not specified	Uncertain significance (Sep 17, 2021)
8-123183209-T-A		not specified	Uncertain significance (Mar 21, 2023)
8-123191803-G-A		not specified	Uncertain significance (Aug 17, 2022)
8-123191830-A-T		not specified	Uncertain significance (Mar 07, 2024)
8-123191842-A-G		not specified	Uncertain significance (Feb 27, 2024)
8-123191860-G-C		not specified	Uncertain significance (May 23, 2023)
8-123194027-A-G		not specified	Uncertain significance (Jan 02, 2024)
8-123194040-G-A		not specified	Uncertain significance (Jun 09, 2022)
8-123194130-T-C		not specified	Uncertain significance (Dec 28, 2022)
8-123207233-G-C		not specified	Uncertain significance (Jun 27, 2023)
8-123207248-C-T		not specified	Uncertain significance (Nov 12, 2021)
8-123207252-A-G		not specified	Uncertain significance (Jan 04, 2024)
8-123207276-G-T		not specified	Uncertain significance (Sep 26, 2023)
8-123207392-G-T		not specified	Uncertain significance (Feb 11, 2022)
8-123207416-G-C		not specified	Likely benign (Jan 31, 2024)
8-123207419-A-G		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM83A	protein_coding	protein_coding	ENST00000518448	4	31115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.03e-7	0.328	124316	3	1429	125748	0.00571

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.483	251	273	0.918	0.0000182	2776
Missense in Polyphen		95	85.749	1.1079		913
Synonymous	0.866	113	125	0.902	0.00000888	931
Loss of Function	0.491	11	12.9	0.852	5.48e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00955	0.00945
Ashkenazi Jewish	0.0101	0.0101
East Asian	0.000163	0.000163
Finnish	0.00569	0.00519
European (Non-Finnish)	0.00772	0.00740
Middle Eastern	0.000163	0.000163
South Asian	0.00154	0.00150
Other	0.00747	0.00719

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable proto-oncogene that functions in the epidermal growth factor receptor/EGFR signaling pathway. Activates both RAS/MAPK and PI3K/AKT/TOR signaling cascades downstream of EGFR. Required for the RAS/MAPK signaling cascade activation upon EGFR stimulation, it also activates both signaling cascades independently of EGFR activation. {ECO:0000269|PubMed:22886303}.

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.862
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.3

Haploinsufficiency Scores

• pHI: 0.242
• hipred: N
• hipred_score: 0.265
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.552

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Fam83a

Gene ontology

• Biological process: epidermal growth factor receptor signaling pathway;cell population proliferation
• Cellular component: cytoplasm
• Molecular function: protein binding;protein kinase binding;phosphatidylinositol 3-kinase regulatory subunit binding