SSX5

SSX family member 5, the group of SSX family

Basic information

Region (hg38): X:48186220-48196795

Links

ENSG00000165583 ∙ NCBI:6758 ∙ OMIM:300327 ∙ HGNC:11339 ∙ Uniprot:O60225 ∙ 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 SSX5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSX5 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			22	5		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	2		6
Total	0	0	26	8	0

Variants in SSX5

This is a list of pathogenic ClinVar variants found in the SSX5 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-48187636-C-G		not specified	Uncertain significance (May 18, 2023)
X-48187661-C-A		not specified	Uncertain significance (Mar 19, 2024)
X-48187692-C-T		not specified	Uncertain significance (Dec 09, 2024)
X-48187720-C-T		not specified	Uncertain significance (Sep 22, 2022)
X-48190157-A-G		not specified	Uncertain significance (May 24, 2023)
X-48190180-C-T		not specified	Uncertain significance (Dec 30, 2024)
X-48190198-T-G		not specified	Uncertain significance (Mar 11, 2024)
X-48190252-G-A		not specified	Uncertain significance (Oct 24, 2023)
X-48190264-G-A		not specified	Likely benign (Nov 25, 2024)
X-48192246-C-T		not specified	Likely benign (Jul 14, 2021)
X-48192247-C-A		not specified	Uncertain significance (Jul 14, 2021)
X-48192251-A-G		not specified	Uncertain significance (Sep 29, 2022)
X-48192272-G-T		not specified	Uncertain significance (Oct 08, 2024)
X-48192275-T-C		not specified	Likely benign (Mar 25, 2024)
X-48192346-A-T			Likely benign (Dec 01, 2022)
X-48192349-T-C			Likely benign (Dec 01, 2022)
X-48194140-C-T		not specified	Likely benign (Jan 24, 2025)
X-48194141-G-T		not specified	Uncertain significance (Nov 10, 2022)
X-48194150-C-T		not specified	Uncertain significance (Jan 23, 2023)
X-48194169-C-G		not specified	Uncertain significance (Dec 05, 2024)
X-48194170-T-C		not specified	Uncertain significance (Jan 08, 2024)
X-48194170-T-G		not specified	Uncertain significance (Dec 05, 2024)
X-48194185-C-T		not specified	Likely benign (Oct 27, 2021)
X-48194194-C-T		not specified	Uncertain significance (Nov 11, 2024)
X-48194204-G-A		not specified	Uncertain significance (Jan 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSX5	protein_coding	protein_coding	ENST00000311798	7	10544

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.05e-8	0.0521	125636	32	67	125735	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.31	134	97.7	1.37	0.00000804	1521
Missense in Polyphen		24	25.062	0.95762		491
Synonymous	-3.20	59	35.0	1.69	0.00000305	402
Loss of Function	-0.675	11	8.84	1.24	5.57e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00690	0.00543
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000991	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000625	0.0000327
Other	0.000251	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0768

Intolerance Scores

• loftool: 0.950
• rvis_EVS: 1.51
• rvis_percentile_EVS: 95.41

Haploinsufficiency Scores

• pHI: 0.0713
• hipred: N
• hipred_score: 0.112
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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
• Cellular component: nucleus
• Molecular function: nucleic acid binding;protein binding