SSX7

protein-coding

SSX family member 7, the group of SSX family

Gene summary

The product of this gene belongs to the family of highly homologous synovial sarcoma X (SSX) breakpoint proteins. These proteins may function as transcriptional repressors. They are also capable of eliciting spontaneously humoral and cellular immune responses in cancer patients, and are potentially useful targets in cancer vaccine-based immunotherapy. SSX1, SSX2 and SSX4 genes have been involved in the t(X;18) translocation characteristically found in all synovial sarcomas. This gene appears not to be involved in this type of chromosome translocation. [provided by RefSeq, Jul 2008]

MANE transcript

NM_173358.2

Inheritance

—

ClinVar variants

U:41B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.12

Max pathogenic AF

—

Genomic locus

chrX:52,644,061-52,654,900

External References & Databases

Ensembl (ENSG00000187754)

Transcript & Mutation Effects

hg38 • Region Span ~10.8 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 SSX7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173358.2. 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 clinvar		2
missense			38 clinvar	4 clinvar	2 clinvar	44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar	1 clinvar		3
Total	0	0	41	6	2	49

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173358.2	RefSeq	NP_775494.1	6	MANE Select
ENST00000298181.6	Ensembl	ENSP00000298181.5	6	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated

Molecular Function

nucleic acid binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298181
Coding exons: 6
Length: 10811
Individuals with no LoFs: 125504
Homozygous LoFs: 10
Heterozygous LoFs: 19
Defined: 125533
p: 0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.97	123	75.0	1.64	0.00000577	1253
Missense (PolyPhen)		23	13.81	1.6655		299
Synonymous	-0.221	29	27.5	1.05	0.00000239	312
Loss of Function	-0.308	8	7.11	1.12	4.48e-7	138

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000086	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00015	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000025	0.000018	rare
South Asian	0.0015	0.00075	notable
Other	0.00024	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Could act as a modulator of transcription.;

Intolerance Scores

LoFtool: 0.830
RVIS EVS: 0.77
RVIS percentile EVS: 87.01

Essentials

Essential (CRISPR): 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