FAM98A

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

Basic information

Region (hg38): 2:33532744-33599347

Links

ENSG00000119812 ∙ NCBI:25940 ∙ ∙ HGNC:24520 ∙ Uniprot:Q8NCA5 ∙ 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 FAM98A gene.

• not_specified (77 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM98A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015475.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			76	1		77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	2	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM98A	protein_coding	protein_coding	ENST00000238823	8	15725

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.547	0.453	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0637	291	288	1.01	0.0000160	3316
Missense in Polyphen		61	76.342	0.79904		899
Synonymous	-0.861	116	105	1.11	0.00000579	1043
Loss of Function	3.91	6	28.5	0.210	0.00000175	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000625	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positively stimulates PRMT1-induced protein arginine methylation (PubMed:28040436). Involved in skeletal homeostasis (By similarity). Positively regulates lysosome peripheral distribution and ruffled border formation in osteoclasts (By similarity). Promotes colorectal cancer cell malignancy (PubMed:28040436). {ECO:0000250|UniProtKB:Q3TJZ6, ECO:0000269|PubMed:28040436}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.491
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.49

Haploinsufficiency Scores

• pHI: 0.831
• hipred: Y
• hipred_score: 0.543
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.839

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam98a

Gene ontology

• Biological process: protein methylation;positive regulation of cell population proliferation;positive regulation of gene expression;lysosome localization;positive regulation of ruffle assembly
• Cellular component: tRNA-splicing ligase complex
• Molecular function: RNA binding;protein binding;protein methyltransferase activity