SSX1

SSX family member 1, the group of SSX family

Basic information

Region (hg38): X:48255392-48267444

Links

ENSG00000126752 ∙ NCBI:6756 ∙ OMIM:312820 ∙ HGNC:11335 ∙ Uniprot:Q16384 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure, X-linked, 5 (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure, X-linked, 5	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	36796361

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SSX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSX1 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			24	4		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	24	6	0

Variants in SSX1

This is a list of pathogenic ClinVar variants found in the SSX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-48257254-G-A		not specified	Likely benign (Oct 27, 2023)
X-48257261-T-A		not specified	Uncertain significance (Jul 20, 2022)
X-48257305-A-C			Likely benign (Dec 01, 2022)
X-48257758-A-G		not specified	Uncertain significance (Feb 28, 2025)
X-48257786-G-C		not specified	Uncertain significance (Feb 16, 2023)
X-48257803-T-C		not specified	Uncertain significance (May 18, 2023)
X-48257804-C-T		not specified	Uncertain significance (Nov 07, 2024)
X-48257822-T-A		not specified	Uncertain significance (Mar 21, 2024)
X-48257825-A-G		SSX1-related disorder	Likely benign (Aug 20, 2019)
X-48257832-G-C			Uncertain significance (-)
X-48257835-A-C		not specified	Uncertain significance (Mar 02, 2023)
X-48257840-A-G		Spermatogenic failure, X-linked, 5	Pathogenic (Mar 16, 2023)
X-48257858-T-A		not specified	Uncertain significance (Aug 02, 2021)
X-48257858-T-G		not specified	Uncertain significance (Feb 12, 2025)
X-48257864-A-G		SSX1-related disorder	Likely benign (Nov 16, 2019)
X-48258535-GGT-G		Spermatogenic failure, X-linked, 5	Pathogenic (Mar 16, 2023)
X-48258544-G-C		not specified	Uncertain significance (Mar 07, 2025)
X-48258562-A-G		not specified	Uncertain significance (Sep 11, 2024)
X-48258563-T-C		not specified	Uncertain significance (May 08, 2024)
X-48258568-A-G		not specified	Uncertain significance (Sep 09, 2021)
X-48258593-G-A		not specified	Uncertain significance (Oct 06, 2023)
X-48258608-A-G		not specified	Uncertain significance (Sep 01, 2021)
X-48258620-G-A		not specified	Likely benign (Aug 13, 2021)
X-48258620-G-C		not specified	Uncertain significance (Aug 27, 2024)
X-48261756-T-C		SSX1-related disorder	Likely benign (Apr 29, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSX1	protein_coding	protein_coding	ENST00000376919	6	12128

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.69e-45	8.37e-14	125650	36	56	125742	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.37	176	71.7	2.45	0.00000533	1264
Missense in Polyphen		40	12.829	3.118		280
Synonymous	-0.567	32	28.2	1.14	0.00000246	301
Loss of Function	-13.4	45	6.92	6.50	4.36e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00127	0.00119
Ashkenazi Jewish	0.000134	0.0000992
East Asian	0.000651	0.000489
Finnish	0.000125	0.0000924
European (Non-Finnish)	0.000405	0.000290
Middle Eastern	0.000651	0.000489
South Asian	0.00105	0.000621
Other	0.000221	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could act as a modulator of transcription.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.871
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.41

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription, DNA-templated;negative regulation of nucleic acid-templated transcription
• Cellular component: nucleus
• Molecular function: nucleic acid binding;transcription corepressor activity;protein binding