SSBP3

single stranded DNA binding protein 3, the group of Wnt enhanceosome complex

Basic information

Region (hg38): 1:54225431-54413479

Links

ENSG00000157216 ∙ NCBI:23648 ∙ OMIM:607390 ∙ HGNC:15674 ∙ Uniprot:Q9BWW4 ∙ 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 SSBP3 gene.

• Inborn genetic diseases (10 variants)
• not provided (1 variants)
• Developmental disorder (1 variants)
• Neurodevelopmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSBP3 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			10			10
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in SSBP3

This is a list of pathogenic ClinVar variants found in the SSBP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-54228299-C-T		not specified	Uncertain significance (Jan 04, 2024)
1-54228773-C-G		not specified	Uncertain significance (Mar 28, 2023)
1-54228816-C-G		not specified	Uncertain significance (Nov 18, 2022)
1-54240909-G-A			Likely benign (Jul 01, 2022)
1-54242199-C-CA		Developmental disorder	Uncertain significance (Jan 13, 2022)
1-54242207-G-A		not specified	Uncertain significance (Nov 30, 2021)
1-54243284-T-C		not specified	Uncertain significance (Jan 09, 2024)
1-54243287-C-T		not specified	Uncertain significance (Jul 20, 2022)
1-54251844-G-A		not specified	Uncertain significance (Feb 10, 2022)
1-54257146-G-A		not specified	Uncertain significance (Feb 05, 2024)
1-54257149-G-A		not specified	Uncertain significance (Jun 09, 2022)
1-54257165-C-T		not specified	Uncertain significance (Dec 26, 2023)
1-54258109-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-54281481-T-C		not specified	Uncertain significance (Apr 07, 2022)
1-54404589-GC-G		Neurodevelopmental disorder	Uncertain significance (Jul 13, 2021)
1-54404878-C-T		not specified	Uncertain significance (Dec 28, 2023)
1-54406001-G-A		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSBP3	protein_coding	protein_coding	ENST00000371320	18	188048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000321	125722	0	2	125724	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.75	117	236	0.496	0.0000133	2502
Missense in Polyphen		41	88.829	0.46156		929
Synonymous	-1.32	112	95.6	1.17	0.00000733	745
Loss of Function	4.90	2	31.9	0.0627	0.00000180	331

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000104	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcription regulation of the alpha 2(I) collagen gene where it binds to the single-stranded polypyrimidine sequences in the promoter region. {ECO:0000250}.

Recessive Scores

• pRec: 0.0839

Intolerance Scores

• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

• pHI: 0.155
• hipred: Y
• hipred_score: 0.749
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.966

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ssbp3
• Phenotype: cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; embryo phenotype; skeleton phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: ssbp3a
• Affected structure: Rohon-Beard neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation;positive regulation of cell population proliferation;prechordal plate formation;midbrain-hindbrain boundary initiation;positive regulation of transcription by RNA polymerase II;head development;head morphogenesis;protein-containing complex assembly;positive regulation of anterior head development
• Cellular component: nucleus;protein-containing complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;single-stranded DNA binding;protein binding