TYMSOS

TYMS opposite strand RNA, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 18:630886-658352

Previous symbols: [ "C18orf56" ]

Links

ENSG00000176912 ∙ NCBI:494514 ∙ ∙ HGNC:29553 ∙ Uniprot:Q8TAI1 ∙ 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 TYMSOS gene.

• Inborn genetic diseases (9 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TYMSOS 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding			9		1	10
Total	0	0	9	1	1

Variants in TYMSOS

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

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

Position	Type	Phenotype	Significance	ClinVar
18-633326-G-T		not specified	Uncertain significance (Jan 30, 2024)
18-633327-A-T		not specified	Uncertain significance (Jan 30, 2024)
18-633345-A-G		not specified	Uncertain significance (Jun 29, 2022)
18-633366-G-T		not specified	Uncertain significance (Nov 17, 2022)
18-633370-A-G		not specified	Uncertain significance (Mar 05, 2024)
18-641341-C-A		not specified	Uncertain significance (Jul 09, 2021)
18-641365-G-A		not specified	Uncertain significance (Mar 28, 2023)
18-641536-A-G		not specified	Uncertain significance (Apr 24, 2023)
18-644962-T-C		not specified	Uncertain significance (Dec 07, 2023)
18-645034-C-T		not specified	Uncertain significance (Dec 13, 2022)
18-657752-G-T		not specified	Uncertain significance (Jul 15, 2021)
18-657785-C-T		TYMS-related disorder	Benign (Feb 21, 2019)
18-657812-C-A		not specified	Uncertain significance (Aug 02, 2021)
18-657827-G-A		not specified	Uncertain significance (Feb 10, 2022)
18-657838-G-A			Likely benign (Aug 05, 2018)
18-657878-A-C		TYMS-related disorder	Likely benign (Dec 29, 2022)
18-658147-C-A			Benign (Jun 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TYMSOS	protein_coding	protein_coding	ENST00000323813	1	17021

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.158	0.650	103767	0	2	103769	0.00000964

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.936	44	65.3	0.674	0.00000312	715
Missense in Polyphen		8	6.8467	1.1684		74
Synonymous	1.64	18	29.3	0.614	0.00000137	301
Loss of Function	0.737	1	2.17	0.460	9.46e-8	20

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000855	0.0000855
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000108	0.0000108
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0640
• hipred: N
• hipred_score: 0.238

Essentials

• essential_gene_gene_trap: N

Gene ontology

• Molecular function: protein binding