SSBP1

single stranded DNA binding protein 1

Basic information

Region (hg38): 7:141738334-141787922

Links

ENSG00000106028

∙ NCBI:6742 ∙ OMIM:600439 ∙ HGNC:11317 ∙ Uniprot:Q04837 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

optic atrophy 13 with retinal and foveal abnormalities (Moderate), mode of inheritance: AD
optic atrophy 13 with retinal and foveal abnormalities (Strong), mode of inheritance: AD
Leigh syndrome (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Optic atrophy 13 with retinal and foveal abnormalities	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Neurologic; Ophthalmologic; Renal	31298765; 31550237; 31550240

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SSBP1 gene.

Inborn_genetic_diseases (10 variants)
not_provided (7 variants)
Optic_atrophy_13_with_retinal_and_foveal_abnormalities (4 variants)
Retinal_dystrophy (1 variants)
Cone-rod_dystrophy (1 variants)
Optic_atrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSBP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003143.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense	3 clinvar	1 clinvar	14 clinvar	1 clinvar		19
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	3	1	14	1	0

Highest pathogenic variant AF is 0.0000013681

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSBP1	protein_coding	protein_coding	ENST00000481508	6	49602

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00364	0.959	125732	0	9	125741	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	56	84.7	0.661	0.00000468	953
Missense in Polyphen		3	22.629	0.13257		313
Synonymous	-0.391	30	27.4	1.10	0.00000142	277
Loss of Function	1.82	6	13.1	0.458	9.48e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000177	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: This protein binds preferentially and cooperatively to ss-DNA. Probably involved in mitochondrial DNA replication. Associates with mitochondrial DNA.;
Pathway: Mismatch repair - Homo sapiens (human);DNA replication - Homo sapiens (human);Homologous recombination - Homo sapiens (human);Mitochondrial biogenesis (Consensus)

Recessive Scores

pRec: 0.161

Intolerance Scores

loftool: 0.418
rvis_EVS: -0.05
rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

pHI: 0.216
hipred: N
hipred_score: 0.459
ghis: 0.570

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ssbp1
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);

Gene ontology

Biological process: mitochondrial DNA replication;mitochondrion organization;positive regulation of helicase activity;mitochondrion morphogenesis
Cellular component: nucleus;mitochondrion;mitochondrial matrix;nucleoid;mitochondrial nucleoid;extracellular exosome
Molecular function: chromatin binding;single-stranded DNA binding;RNA binding;protein binding