FAM98A

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

Basic information

Region (hg38): 2:33532743-33599347

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.

• Inborn genetic diseases (22 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.

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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in FAM98A

This is a list of pathogenic ClinVar variants found in the FAM98A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-33534350-G-C		not specified	Uncertain significance (Aug 22, 2023)
2-33539176-C-A		not specified	Uncertain significance (Jan 04, 2022)
2-33543528-A-G		not specified	Uncertain significance (Jul 20, 2021)
2-33543599-G-A		not specified	Uncertain significance (Nov 03, 2023)
2-33549666-A-G		not specified	Uncertain significance (Feb 13, 2024)
2-33549709-G-T		not specified	Uncertain significance (Mar 05, 2024)
2-33549712-C-T			Likely benign (Aug 14, 2018)
2-33558223-A-G		not specified	Uncertain significance (Jun 26, 2023)
2-33558277-G-A		not specified	Uncertain significance (Nov 08, 2022)
2-33558325-C-G		not specified	Uncertain significance (Jul 15, 2021)
2-33558687-T-C		not specified	Uncertain significance (Feb 28, 2023)
2-33558746-G-A		not specified	Uncertain significance (Sep 20, 2023)
2-33558758-T-C		not specified	Uncertain significance (Dec 09, 2023)
2-33558761-C-T		not specified	Uncertain significance (Mar 29, 2023)
2-33558897-C-T		not specified	Uncertain significance (Apr 24, 2023)
2-33558917-G-T		not specified	Uncertain significance (Feb 22, 2023)
2-33558948-A-G		not specified	Uncertain significance (Feb 13, 2024)
2-33558971-C-T		not specified	Uncertain significance (Feb 15, 2023)
2-33584835-G-C		not specified	Uncertain significance (Mar 07, 2024)
2-33584852-A-T		not specified	Uncertain significance (Aug 28, 2023)
2-33584933-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-33584945-C-T		not specified	Uncertain significance (Aug 14, 2023)
2-33584951-C-T		not specified	Uncertain significance (Apr 12, 2023)
2-33584963-C-T		not specified	Uncertain significance (May 27, 2022)
2-33585000-C-T		not specified	Uncertain significance (Oct 22, 2021)

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