FAM50B

family with sequence similarity 50 member B

Basic information

Region (hg38): 6:3849372-3851320

Links

ENSG00000145945 ∙ NCBI:26240 ∙ OMIM:614686 ∙ HGNC:18789 ∙ Uniprot:Q9Y247 ∙ 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 FAM50B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM50B 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in FAM50B

This is a list of pathogenic ClinVar variants found in the FAM50B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-3849845-G-A		not specified	Uncertain significance (May 25, 2022)
6-3849861-T-A		not specified	Uncertain significance (Oct 12, 2021)
6-3849884-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
6-3849891-A-T		not specified	Uncertain significance (Jan 17, 2024)
6-3849920-G-A		not specified	Uncertain significance (Dec 08, 2023)
6-3850064-G-A		not specified	Uncertain significance (Mar 19, 2024)
6-3850094-G-A		not specified	Uncertain significance (Dec 21, 2022)
6-3850124-C-T		not specified	Uncertain significance (Aug 04, 2022)
6-3850125-G-A		not specified	Uncertain significance (Nov 07, 2022)
6-3850143-G-A		not specified	Uncertain significance (Apr 15, 2024)
6-3850280-G-A		not specified	Uncertain significance (Feb 15, 2023)
6-3850304-C-T		not specified	Uncertain significance (Dec 28, 2022)
6-3850319-C-T		not specified	Uncertain significance (Dec 15, 2023)
6-3850326-A-G		not specified	Uncertain significance (Dec 28, 2022)
6-3850382-T-C		not specified	Uncertain significance (Feb 02, 2022)
6-3850410-C-T		not specified	Uncertain significance (Mar 21, 2022)
6-3850413-T-G		not specified	Uncertain significance (Dec 21, 2023)
6-3850416-G-A		not specified	Uncertain significance (Aug 19, 2021)
6-3850757-G-A		not specified	Uncertain significance (Jun 01, 2023)
6-3850764-A-C		not specified	Uncertain significance (Aug 22, 2023)
6-3850772-A-G		not specified	Uncertain significance (Jun 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM50B	protein_coding	protein_coding	ENST00000380274	1	1932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.154	0.831	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.31	149	252	0.591	0.0000197	2122
Missense in Polyphen		39	82.589	0.47222		747
Synonymous	1.69	95	118	0.803	0.0000100	635
Loss of Function	2.10	3	10.3	0.292	5.25e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.268
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.312
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.931

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam50b

Gene ontology

• Cellular component: nucleoplasm;intercellular bridge
• Molecular function: protein binding