FAM89B

family with sequence similarity 89 member B

Basic information

Region (hg38): 11:65572349-65574198

Links

ENSG00000176973 ∙ NCBI:23625 ∙ OMIM:616128 ∙ HGNC:16708 ∙ Uniprot:Q8N5H3 ∙ 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 FAM89B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM89B 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			13	3		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	3	0

Variants in FAM89B

This is a list of pathogenic ClinVar variants found in the FAM89B region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65572676-G-A		not specified	Uncertain significance (Oct 12, 2024)
11-65572701-G-A		not specified	Uncertain significance (Sep 27, 2024)
11-65572710-G-C		not specified	Uncertain significance (Feb 07, 2025)
11-65572772-G-T		not specified	Uncertain significance (Jun 24, 2022)
11-65572799-G-T		not specified	Uncertain significance (Mar 04, 2025)
11-65572844-G-A		not specified	Uncertain significance (Oct 07, 2024)
11-65572874-G-T		not specified	Uncertain significance (Jan 26, 2023)
11-65572875-C-T		not specified	Uncertain significance (Jan 23, 2025)
11-65572881-C-T		not specified	Uncertain significance (Jul 14, 2021)
11-65572902-C-T		not specified	Uncertain significance (Mar 08, 2024)
11-65572913-C-A		not specified	Uncertain significance (Sep 27, 2024)
11-65572916-C-T		not specified	Uncertain significance (Jun 09, 2022)
11-65573441-C-T		not specified	Likely benign (Sep 10, 2024)
11-65573462-T-C		not specified	Uncertain significance (May 04, 2023)
11-65573479-C-T		not specified	Likely benign (Mar 01, 2024)
11-65573515-G-A		not specified	Likely benign (Jun 21, 2023)
11-65573543-G-A		not specified	Uncertain significance (Jun 21, 2022)
11-65573604-A-C		not specified	Uncertain significance (Oct 05, 2021)
11-65573630-A-G		not specified	Uncertain significance (Aug 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM89B	protein_coding	protein_coding	ENST00000530349	2	1850

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0523	0.712	125569	0	5	125574	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	35	57.4	0.609	0.00000316	1192
Missense in Polyphen		21	39.7	0.52897		694
Synonymous	0.186	27	28.3	0.955	0.00000176	416
Loss of Function	0.699	2	3.39	0.590	1.45e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000185	0.0000176
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates TGF-beta-induced signaling; in cooperation with SKI prevents the translocation of SMAD2 from the nucleus to the cytoplasm in response to TGF-beta. Acts as an adapter that mediates the specific recognition of LIMK1 by CDC42BPA and CDC42BPB in the lamellipodia. LRAP25-mediated CDC42BPA/CDC42BPB targeting to LIMK1 and the lamellipodium results in LIMK1 activation and the subsequent phosphorylation of CFL1 which is important for lamellipodial F-actin regulation. {ECO:0000250|UniProtKB:Q9QUI1}.

Haploinsufficiency Scores

• pHI: 0.154
• hipred: N
• hipred_score: 0.291
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam89b

Gene ontology

• Biological process: establishment of cell polarity;positive regulation of cell migration;negative regulation of transforming growth factor beta receptor signaling pathway;negative regulation of SMAD protein signal transduction
• Cellular component: cytoplasm;lamellipodium
• Molecular function: transcription corepressor binding