FAM98B

family with sequence similarity 98 member B, the group of tRNA splicing ligase complex

Basic information

Region (hg38): 15:38454127-38487710

Links

ENSG00000171262 ∙ NCBI:283742 ∙ OMIM:616142 ∙ HGNC:26773 ∙ Uniprot:Q52LJ0 ∙ 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 FAM98B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM98B 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				1		1
missense			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	0

Variants in FAM98B

This is a list of pathogenic ClinVar variants found in the FAM98B region.

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

Position	Type	Phenotype	Significance	ClinVar
15-38454207-G-A		not specified	Uncertain significance (Aug 04, 2024)
15-38464075-G-A		not specified	Uncertain significance (Oct 21, 2021)
15-38464135-A-T		not specified	Uncertain significance (Jan 30, 2024)
15-38464147-T-C		not specified	Uncertain significance (Nov 02, 2023)
15-38464169-C-T		not specified	Uncertain significance (Feb 27, 2023)
15-38464175-C-T		not specified	Uncertain significance (Jan 27, 2025)
15-38465275-A-T		not specified	Uncertain significance (Jan 17, 2024)
15-38465356-A-G		not specified	Uncertain significance (Feb 19, 2025)
15-38465359-T-C		not specified	Uncertain significance (Mar 16, 2024)
15-38465367-C-T		not specified	Uncertain significance (Jul 13, 2021)
15-38470349-A-G		not specified	Likely benign (Jul 16, 2024)
15-38473515-T-C		not specified	Uncertain significance (Nov 07, 2024)
15-38474230-C-T		not specified	Uncertain significance (Dec 20, 2023)
15-38474231-G-A		not specified	Uncertain significance (Feb 23, 2023)
15-38474234-G-A		not specified	Uncertain significance (Oct 01, 2024)
15-38474260-G-A		not specified	Uncertain significance (May 31, 2023)
15-38481293-T-G		not specified	Uncertain significance (Jun 07, 2022)
15-38481344-C-T		not specified	Uncertain significance (Mar 06, 2023)
15-38481383-C-T		not specified	Uncertain significance (Sep 18, 2024)
15-38481389-A-T		not specified	Uncertain significance (Dec 09, 2023)
15-38481394-C-G		not specified	Uncertain significance (Mar 08, 2024)
15-38481441-C-T		not specified	Likely benign (Mar 07, 2025)
15-38484292-C-T		not specified	Uncertain significance (Sep 25, 2024)
15-38484306-C-T		not specified	Uncertain significance (Nov 20, 2023)
15-38484367-G-A		not specified	Uncertain significance (Aug 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM98B	protein_coding	protein_coding	ENST00000397609	8	33584

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0103	0.988	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.441	184	202	0.913	0.0000105	2711
Missense in Polyphen		73	83.607	0.87313		1067
Synonymous	0.396	65	69.2	0.939	0.00000348	859
Loss of Function	2.72	7	20.2	0.346	0.00000115	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000543	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000667	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positively stimulates PRMT1-induced protein arginine dimethylated arginine methylation (PubMed:28040436). Promotes colorectal cancer cell malignancy (PubMed:28040436). {ECO:0000269|PubMed:28040436}.
• Pathway: tRNA processing;Metabolism of RNA;tRNA processing in the nucleus (Consensus)

Recessive Scores

• pRec: 0.0833

Intolerance Scores

• loftool: 0.509
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.132
• hipred: Y
• hipred_score: 0.640
• ghis: 0.668

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.793

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam98b

Gene ontology

• Biological process: protein methylation;positive regulation of cell population proliferation;positive regulation of gene expression
• Cellular component: nucleus;nucleoplasm;cytoplasm;intracellular membrane-bounded organelle;tRNA-splicing ligase complex
• Molecular function: RNA binding;protein binding;protein methyltransferase activity;identical protein binding