SSX7

SSX family member 7, the group of SSX family

Basic information

Region (hg38): X:52644061-52654900

Links

ENSG00000187754 ∙ NCBI:280658 ∙ OMIM:300542 ∙ HGNC:19653 ∙ Uniprot:Q7RTT5 ∙ 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 SSX7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSX7 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	2	2	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region				1		1
non coding						0
Total	0	0	24	4	2

Variants in SSX7

This is a list of pathogenic ClinVar variants found in the SSX7 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-52645449-G-C		not specified	Uncertain significance (Jul 20, 2021)
X-52645457-C-T			Benign (Dec 31, 2019)
X-52645458-T-C			Likely benign (Dec 18, 2018)
X-52645487-C-A		not specified	Uncertain significance (Dec 04, 2024)
X-52645494-C-G		not specified	Uncertain significance (Mar 14, 2023)
X-52645499-T-C		not specified	Uncertain significance (Dec 05, 2024)
X-52645504-C-T		not specified	Uncertain significance (Jun 28, 2024)
X-52645516-G-A			Benign (Jul 02, 2018)
X-52645523-C-T		not specified	Uncertain significance (Jul 12, 2023)
X-52645529-T-C		not specified	Uncertain significance (Jul 27, 2021)
X-52645545-T-C			Likely benign (Dec 31, 2019)
X-52648271-G-T		not specified	Uncertain significance (Oct 02, 2023)
X-52648293-G-C		not specified	Uncertain significance (Jul 07, 2022)
X-52648293-G-T		not specified	Uncertain significance (Aug 30, 2022)
X-52648295-T-G		not specified	Uncertain significance (Sep 16, 2021)
X-52648305-G-A		not specified	Uncertain significance (Oct 27, 2023)
X-52648333-A-G		not specified	Likely benign (Apr 14, 2022)
X-52648342-C-T		not specified	Likely benign (Nov 03, 2023)
X-52648359-G-C		not specified	Uncertain significance (Jan 10, 2022)
X-52650363-A-G		not specified	Uncertain significance (Jun 28, 2022)
X-52650396-C-T		not specified	Uncertain significance (Oct 18, 2021)
X-52652261-C-T		not specified	Uncertain significance (Feb 23, 2023)
X-52652262-T-G		not specified	Uncertain significance (Feb 23, 2023)
X-52652280-A-C		not specified	Uncertain significance (May 11, 2022)
X-52652294-G-C		not specified	Uncertain significance (Oct 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSX7	protein_coding	protein_coding	ENST00000298181	6	10811

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000268	0.180	125504	10	19	125533	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.97	123	75.0	1.64	0.00000577	1253
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000858	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.000145	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000245	0.0000176
Middle Eastern	0.000145	0.000109
South Asian	0.00152	0.000753
Other	0.000243	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0505
• hipred: N
• hipred_score: 0.112
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

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