TSTD2

protein-coding

thiosulfate sulfurtransferase like domain containing 2

Gene summary

Predicted to enable transferase activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf97

MANE transcript

NM_139246.5

Inheritance

—

ClinVar variants

U:89B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr9:97,600,080-97,633,368

External References & Databases

Ensembl (ENSG00000136925)

Transcript & Mutation Effects

hg38 • Region Span ~33.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TSTD2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_139246.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			82 clinvar	5 clinvar		87
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	89	5	0	94

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_139246.5	RefSeq	NP_640339.4	9	MANE Select
ENST00000341170.5	Ensembl	ENSP00000342499.4	9	MANE Select
ENST00000375165.5	Ensembl	ENSP00000364308.2	1	Standard
ENST00000375172.6	Ensembl	ENSP00000364315.3	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function
protein binding

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000341170
Coding exons: 9
Length: 33601
Individuals with no LoFs: 125535
Homozygous LoFs: 0
Heterozygous LoFs: 213
Defined: 125748
p: 0.000847

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0248	277	278	0.996	0.0000142	3414
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0012	notable
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00044	0.00044	rare
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.0013	0.0013	notable
South Asian	0.00044	0.00042	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0787

Intolerance Scores

LoFtool: 0.871
RVIS EVS: 0.58
RVIS percentile EVS: 82.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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