TSTD2

thiosulfate sulfurtransferase like domain containing 2

Basic information

Region (hg38): 9:97600080-97633368

Previous symbols: [ "C9orf97" ]

Links

ENSG00000136925 ∙ NCBI:158427 ∙ ∙ HGNC:30087 ∙ Uniprot:Q5T7W7 ∙ 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 TSTD2 gene.

• not_specified (81 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSTD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000139246.5. 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						0
missense			76	5		81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	5	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSTD2	protein_coding	protein_coding	ENST00000341170	9	33601

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.90e-11	0.221	125535	0	213	125748	0.000847

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0248	277	278	0.996	0.0000142	3414
Missense in Polyphen		110	106.76	1.0304		1274
Synonymous	0.638	91	99.1	0.918	0.00000482	932
Loss of Function	0.836	19	23.4	0.813	0.00000114	303

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00173	0.00172
Ashkenazi Jewish	0.00	0.00
East Asian	0.000437	0.000435
Finnish	0.0000938	0.0000924
European (Non-Finnish)	0.00132	0.00131
Middle Eastern	0.000437	0.000435
South Asian	0.000440	0.000425
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0787

Intolerance Scores

• loftool: 0.871
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.25

Haploinsufficiency Scores

• pHI: 0.0963
• hipred: N
• hipred_score: 0.251
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tstd2

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function;protein binding