SSBP4

protein-coding

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

Gene summary

Predicted to enable transcription coactivator activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_032627.5

Inheritance

—

ClinVar variants

U:83B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr19:18,418,864-18,434,562

External References & Databases

Ensembl (ENSG00000130511)

Transcript & Mutation Effects

hg38 • Region Span ~15.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SSBP4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 76

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032627.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			77 clinvar	2 clinvar		79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	83	4	0	87

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 55 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032627.5	RefSeq	NP_116016.1	18	MANE Select
ENST00000270061.12	Ensembl	ENSP00000270061.5	18	MANE Select
NM_001009998.4	RefSeq	NP_001009998.1	17	Standard
ENST00000348495.10	Ensembl	ENSP00000252807.7	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of transcription by RNA polymerase II

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
single-stranded DNA binding
protein binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000270061
Coding exons: 18
Length: 15699
Individuals with no LoFs: 125687
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125695
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.333	212	226	0.938	0.0000139	2446
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000031	0.000029	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.000061	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.130
RVIS EVS: -0.29
RVIS percentile EVS: 32.94

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.932

Gene Damage Prediction

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