FAM209B

family with sequence similarity 209 member B

Basic information

Region (hg38): 20:56533245-56536520

Previous symbols: [ "C20orf107" ]

Links

ENSG00000213714 ∙ NCBI:388799 ∙ ∙ HGNC:16101 ∙ Uniprot:Q5JX69 ∙ 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 FAM209B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM209B 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in FAM209B

This is a list of pathogenic ClinVar variants found in the FAM209B region.

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

Position	Type	Phenotype	Significance	ClinVar
20-56533429-A-G		not specified	Uncertain significance (Feb 12, 2024)
20-56533430-G-T		not specified	Uncertain significance (Jul 21, 2022)
20-56533481-A-G		not specified	Uncertain significance (Dec 15, 2023)
20-56533495-A-G		not specified	Likely benign (Feb 28, 2023)
20-56533517-A-G		not specified	Uncertain significance (Feb 16, 2023)
20-56536185-C-T		not specified	Uncertain significance (Feb 16, 2023)
20-56536229-C-A		not specified	Uncertain significance (Mar 31, 2023)
20-56536236-C-T		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM209B	protein_coding	protein_coding	ENST00000371325	2	3275

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000180	0.283	123621	80	2046	125747	0.00849

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.453	79	91.2	0.867	0.00000502	1113
Missense in Polyphen		27	33.104	0.8156		451
Synonymous	-0.0231	35	34.8	1.00	0.00000207	325
Loss of Function	-0.511	5	3.91	1.28	1.70e-7	40

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0272	0.0230
Ashkenazi Jewish	0.0239	0.0119
East Asian	0.00452	0.00223
Finnish	0.00205	0.00129
European (Non-Finnish)	0.0197	0.00967
Middle Eastern	0.00452	0.00223
South Asian	0.0240	0.0120
Other	0.0305	0.0149

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.9
• rvis_percentile_EVS: 89.39

Haploinsufficiency Scores

• pHI: 0.00817
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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

• Cellular component: nucleus;integral component of membrane