SSBP4

single stranded DNA binding protein 4, the group of Wnt enhanceosome complex

Basic information

Region (hg38): 19:18418864-18434562

Links

ENSG00000130511 ∙ NCBI:170463 ∙ OMIM:607391 ∙ HGNC:15676 ∙ Uniprot:Q9BWG4 ∙ 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 SSBP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSBP4 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						0
missense			46			46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	0	0

Variants in SSBP4

This is a list of pathogenic ClinVar variants found in the SSBP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18419661-G-C		not specified	Uncertain significance (Jun 07, 2023)
19-18419665-G-C		not specified	Uncertain significance (Mar 24, 2023)
19-18419705-G-C		not specified	Uncertain significance (Dec 18, 2023)
19-18427395-A-G		not specified	Uncertain significance (Dec 28, 2022)
19-18427786-C-A		not specified	Uncertain significance (Oct 03, 2024)
19-18427954-C-T		not specified	Uncertain significance (Feb 07, 2025)
19-18430853-G-A		not specified	Uncertain significance (Jun 12, 2023)
19-18430880-G-A		not specified	Uncertain significance (Sep 08, 2024)
19-18430910-A-G		not specified	Uncertain significance (Apr 19, 2023)
19-18430911-T-C		not specified	Uncertain significance (Jun 27, 2023)
19-18430914-C-T		not specified	Uncertain significance (Oct 26, 2022)
19-18431362-G-A		not specified	Uncertain significance (Feb 26, 2025)
19-18431380-C-A		not specified	Uncertain significance (Aug 20, 2024)
19-18431408-C-T		not specified	Uncertain significance (Jan 31, 2022)
19-18431647-C-T		not specified	Uncertain significance (Jan 10, 2025)
19-18431660-C-T		not specified	Uncertain significance (Mar 02, 2023)
19-18431662-C-T		not specified	Uncertain significance (Nov 13, 2024)
19-18431680-C-T		not specified	Uncertain significance (Mar 30, 2024)
19-18431693-G-T		not specified	Uncertain significance (Feb 13, 2023)
19-18431794-C-T		not specified	Uncertain significance (Mar 31, 2022)
19-18431799-G-A		not specified	Uncertain significance (Dec 19, 2023)
19-18431799-G-T		not specified	Uncertain significance (Dec 19, 2022)
19-18431826-C-G		not specified	Uncertain significance (Jan 06, 2023)
19-18431845-C-G		not specified	Uncertain significance (Sep 08, 2024)
19-18431854-G-C		not specified	Uncertain significance (Feb 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSBP4	protein_coding	protein_coding	ENST00000270061	18	15699

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.370	0.630	125687	0	8	125695	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.333	212	226	0.938	0.0000139	2446
Missense in Polyphen		66	88.481	0.74593		994
Synonymous	0.163	91	93.0	0.979	0.00000680	758
Loss of Function	3.70	6	26.6	0.226	0.00000146	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000307	0.0000307
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000607	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.0000607	0.0000544
South Asian	0.00	0.00
Other	0.000183	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.130
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.206
• hipred: N
• hipred_score: 0.469
• ghis: 0.652

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.932

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ssbp4

Gene ontology

• Biological process: positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;single-stranded DNA binding;protein binding