SSBP3

protein-coding

single stranded DNA binding protein 3, 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 act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_145716.4

Inheritance

ClinVar variants

U:57B:2

Top phenotype

Neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr1:54,225,432-54,413,479

External References & Databases

Ensembl (ENSG00000157216)

Transcript & Mutation Effects

hg38 • Region Span ~188.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PMGRC

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SSBP3 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 38

not providedTotal: 5

Neurodevelopmental disorderTotal: 1

Syndromic intellectual disabilityTotal: 1

Developmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145716.4. 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 clinvar		4
missense			45 clinvar			45
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	57	2	0	59

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145716.4	RefSeq	NP_663768.1	18	MANE Select
ENST00000610401.6	Ensembl	ENSP00000479674.2	18	MANE Select
NM_001009955.4	RefSeq	NP_001009955.1	17	Standard
NM_001394360.1	RefSeq	NP_001381289.1	17	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ssbp3a	Danio rerio	Structure: Rohon-Beard neuron Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

ssbp3a

Danio rerio

Structure: Rohon-Beard neuron

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

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

Cellular Component

nucleus
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371320
Coding exons: 18
Length: 188048
Individuals with no LoFs: 125722
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125724
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.75	117	236	0.496	0.0000133	2502
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000010	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.966

Gene Damage Prediction

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