SSX3

SSX family member 3, the group of SSX family

Basic information

Region (hg38): X:48346427-48356707

Links

ENSG00000165584 ∙ NCBI:10214 ∙ OMIM:300325 ∙ HGNC:11337 ∙ Uniprot:Q99909 ∙ 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 SSX3 gene.

• not_specified (37 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSX3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021014.4. 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					1	1
missense			31	6		37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	6	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSX3	protein_coding	protein_coding	ENST00000298396	6	10280

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00903	0.821	125723	4	5	125732	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.484	92	79.8	1.15	0.00000650	1254
Missense in Polyphen		6	11.453	0.52389		245
Synonymous	-1.59	38	27.4	1.39	0.00000229	317
Loss of Function	1.09	4	7.13	0.561	4.49e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000433	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000386	0.0000264
Middle Eastern	0.000433	0.000326
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0809

Intolerance Scores

• loftool: 0.580
• rvis_EVS: 0.88
• rvis_percentile_EVS: 89.02

Haploinsufficiency Scores

• pHI: 0.0965
• hipred: N
• hipred_score: 0.112
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.533

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