FAM209A

family with sequence similarity 209 member A

Basic information

Region (hg38): 20:56517186-56526152

Previous symbols: [ "C20orf106" ]

Links

ENSG00000124103 ∙ NCBI:200232 ∙ ∙ HGNC:16100 ∙ Uniprot:Q5JX71 ∙ 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 FAM209A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM209A 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			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	0

Variants in FAM209A

This is a list of pathogenic ClinVar variants found in the FAM209A region.

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

Position	Type	Phenotype	Significance	ClinVar
20-56518145-G-T		not specified	Uncertain significance (Apr 25, 2022)
20-56518152-G-A		not specified	Uncertain significance (Jun 18, 2021)
20-56518158-A-G		not specified	Uncertain significance (Aug 08, 2023)
20-56518228-C-T		not specified	Uncertain significance (Apr 09, 2024)
20-56518233-C-T		not specified	Uncertain significance (Mar 15, 2024)
20-56524816-C-T		not specified	Uncertain significance (Jun 24, 2022)
20-56524828-C-T		not specified	Likely benign (Dec 08, 2023)
20-56524906-A-G		not specified	Uncertain significance (Feb 27, 2023)
20-56524941-C-T		not specified	Uncertain significance (Jan 04, 2022)
20-56525873-C-T		not specified	Uncertain significance (Jul 13, 2021)
20-56525894-A-G		not specified	Uncertain significance (Mar 22, 2023)
20-56525946-G-A		not specified	Uncertain significance (Jul 12, 2022)
20-56525954-A-C		not specified	Uncertain significance (Nov 30, 2022)
20-56525961-C-T		not specified	Uncertain significance (Sep 26, 2022)
20-56525967-C-A		not specified	Uncertain significance (Dec 28, 2022)
20-56526001-G-C		not specified	Likely benign (Oct 26, 2022)
20-56526047-T-C		not specified	Uncertain significance (Jun 09, 2022)
20-56526059-A-G		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM209A	protein_coding	protein_coding	ENST00000371328	2	8956

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0789	0.765	125183	8	556	125747	0.00225

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.345	107	97.4	1.10	0.00000564	1116
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00714	0.00597
Ashkenazi Jewish	0.00119	0.000595
East Asian	0.000707	0.000381
Finnish	0.000884	0.000462
European (Non-Finnish)	0.00599	0.00296
Middle Eastern	0.000707	0.000381
South Asian	0.00435	0.00219
Other	0.0114	0.00572

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.81

Haploinsufficiency Scores

• pHI: 0.00453
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam209

Gene ontology

• Biological process: biological_process
• Cellular component: nucleus;integral component of membrane;extracellular exosome
• Molecular function: molecular_function