FAM98C

family with sequence similarity 98 member C

Basic information

Region (hg38): 19:38403092-38409088

Links

ENSG00000130244 ∙ NCBI:147965 ∙ ∙ HGNC:27119 ∙ Uniprot:Q17RN3 ∙ 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 FAM98C gene.

• Inborn genetic diseases (18 variants)
• not provided (3 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM98C 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			14	4		18
nonsense				1		1
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	14	7	1

Variants in FAM98C

This is a list of pathogenic ClinVar variants found in the FAM98C region.

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

Position	Type	Phenotype	Significance	ClinVar
19-38403152-T-C		FAM98C-related disorder	Likely benign (May 22, 2019)
19-38403178-T-C		not specified	Likely benign (Dec 01, 2022)
19-38403200-A-G		not specified	Likely benign (Apr 06, 2022)
19-38403217-G-C		not specified	Uncertain significance (Nov 07, 2023)
19-38403221-A-G		FAM98C-related disorder	Likely benign (Oct 28, 2019)
19-38403349-T-A		not specified	Uncertain significance (Jul 16, 2021)
19-38403357-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-38403369-G-A		not specified	Uncertain significance (Jan 10, 2022)
19-38403378-T-C		not specified	Uncertain significance (May 03, 2023)
19-38403456-G-A		not specified	Uncertain significance (Jul 09, 2021)
19-38403462-G-A		FAM98C-related disorder	Benign (Apr 16, 2019)
19-38403654-G-T		FAM98C-related disorder	Likely benign (Jul 15, 2019)
19-38403667-G-A		FAM98C-related disorder	Benign (Oct 28, 2019)
19-38404953-G-A		not specified	Uncertain significance (Dec 27, 2023)
19-38404991-G-A		not specified	Uncertain significance (Nov 07, 2022)
19-38405037-C-T		FAM98C-related disorder	Benign (Feb 21, 2019)
19-38405101-G-T		not specified	Uncertain significance (Dec 31, 2023)
19-38405411-C-T		not specified	Uncertain significance (Feb 17, 2023)
19-38405419-T-C		FAM98C-related disorder	Likely benign (Apr 05, 2019)
19-38405522-G-A		not specified	Uncertain significance (Mar 01, 2023)
19-38405524-G-A			Likely benign (Jun 18, 2018)
19-38405561-C-T		not specified	Likely benign (Sep 27, 2021)
19-38405570-C-T		not specified	Uncertain significance (Jun 07, 2023)
19-38405574-GCCT-G		not specified	Likely benign (May 04, 2022)
19-38405589-G-A		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM98C	protein_coding	protein_coding	ENST00000252530	8	5954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-7	0.338	124484	1	329	124814	0.00132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.553	165	186	0.886	0.0000112	2140
Missense in Polyphen		72	77.352	0.93081		863
Synonymous	1.60	61	79.1	0.771	0.00000457	792
Loss of Function	0.592	12	14.4	0.832	7.69e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0132	0.0131
Ashkenazi Jewish	0.000100	0.0000993
East Asian	0.00172	0.00173
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000555	0.000547
Middle Eastern	0.00172	0.00173
South Asian	0.000556	0.000556
Other	0.000497	0.000495

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.784
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.17

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.180
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.655

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam98c

Gene ontology

• Cellular component: tRNA-splicing ligase complex