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.

• Optic atrophy 13 with retinal and foveal abnormalities (2 variants)
• not provided (1 variants)
• Cone-rod dystrophy (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.

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	2	1	5	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	2	1	5	1	0

Variants in SSBP1

This is a list of pathogenic ClinVar variants found in the SSBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-141739179-C-T		Optic atrophy	Uncertain significance (Jan 01, 2022)
7-141739192-T-TA		Retinal dystrophy	Uncertain significance (Jan 01, 2022)
7-141742162-T-A			Likely benign (Jan 01, 2024)
7-141742169-G-A		Inborn genetic diseases	Uncertain significance (Oct 25, 2023)
7-141742176-G-A		Inborn genetic diseases	Likely benign (Sep 01, 2021)
7-141742179-A-G		Inborn genetic diseases	Uncertain significance (Jul 05, 2023)
7-141742205-A-T		Inborn genetic diseases	Uncertain significance (Oct 27, 2023)
7-141743588-G-A		Optic atrophy 13 with retinal and foveal abnormalities • Cone-rod dystrophy	Pathogenic (Jul 24, 2023)
7-141743594-G-T		Optic atrophy 13 with retinal and foveal abnormalities	Likely pathogenic (Apr 20, 2023)
7-141743641-A-G			Uncertain significance (May 01, 2020)
7-141743678-G-C		Inborn genetic diseases	Uncertain significance (May 01, 2024)
7-141743934-A-C		Inborn genetic diseases	Uncertain significance (Sep 08, 2023)
7-141745501-G-A		Optic atrophy 13 with retinal and foveal abnormalities	Pathogenic (Jan 17, 2024)
7-141745528-A-G			Uncertain significance (Oct 01, 2024)
7-141745575-A-G			Uncertain significance (Sep 03, 2020)
7-141750329-G-A		Optic atrophy 13 with retinal and foveal abnormalities	Pathogenic (Sep 03, 2020)
7-141764174-G-A		not specified	Uncertain significance (May 11, 2022)
7-141764176-G-T		not specified	Uncertain significance (Mar 06, 2023)
7-141764238-T-C		not specified	Uncertain significance (Jun 11, 2021)
7-141764279-A-G		not specified	Uncertain significance (Jan 30, 2024)
7-141764296-C-A		not specified	Uncertain significance (Mar 01, 2024)
7-141764313-C-A		not specified	Uncertain significance (Oct 12, 2021)
7-141764313-C-T		not specified	Uncertain significance (Sep 13, 2023)
7-141764348-A-G		not specified	Uncertain significance (Aug 20, 2024)
7-141764504-C-G		not specified	Uncertain significance (Jan 17, 2024)

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