Optic atrophy 13 with retinal and foveal abnormalities

Summary

Optic atrophy 13 with retinal and foveal abnormalities (MONDO:0008135) is a disease caused by SSBP1 (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: SSBP1 (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 4

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	optic atrophy 13 with retinal and foveal abnormalities
Mondo ID	MONDO:0008135
MeSH	C563494
OMIM	165510
UMLS	C5435585
MedGen	1768962
GARD	0024603
Is cancer (heuristic)	no

Also known as: optic atrophy 13 with retinal and foveal abnormalities · optic atrophy with negative Electroretinograms

Data availability: 4 ClinVar variants · 3 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disorder › central nervous system disorder › optic nerve disorder › optic atrophy › primary optic atrophy › hereditary optic atrophy › optic atrophy 13 with retinal and foveal abnormalities

Related subtypes (14): optic atrophy 6, optic atrophy 2, Leber hereditary optic neuropathy, optic atrophy 4, autosomal recessive optic atrophy, OPA7 type, optic atrophy 11, osteogenesis imperfecta-retinopathy-seizures-intellectual disability syndrome, autosomal dominant optic atrophy, optic atrophy 10 with or without ataxia, intellectual disability, and seizures, optic atrophy 12, optic atrophy 14, optic atrophy 15, optic atrophy 16, ACO2-related optic atrophy with or without extraocular features

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

4 retrieved; paginated sample, class counts are floors:

3 pathogenic, 1 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
977502	NM_003143.3(SSBP1):c.113G>A (p.Arg38Gln)	SSBP1	Pathogenic	criteria provided, single submitter
977503	NM_003143.3(SSBP1):c.320G>A (p.Arg107Gln)	SSBP1	Pathogenic	criteria provided, multiple submitters, no conflicts
977504	NM_003143.3(SSBP1):c.422G>A (p.Ser141Asn)	SSBP1	Pathogenic	no assertion criteria provided
977505	NM_003143.3(SSBP1):c.119G>T (p.Gly40Val)	SSBP1	Likely pathogenic	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 3 · Orphanet: 1 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

Gene	Classification	Inheritance	Disease	Records
SSBP1	Strong	Autosomal dominant	optic atrophy 13 with retinal and foveal abnormalities	3

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
SSBP1	Orphanet:90635	Rare autosomal dominant non-syndromic sensorineural deafness type DFNA

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
SSBP1	HGNC:11317	ENSG00000106028	Q04837	Single-stranded DNA-binding protein, mitochondrial	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
SSBP1	Single-stranded DNA-binding protein, mitochondrial	Binds preferentially and cooperatively to pyrimidine rich single-stranded DNA (ss-DNA).

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

Family	Genes	Fold	FDR
Other/Unknown	1	1.8×	0.558

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
SSBP1	Other/Unknown	no		Primosome_PriB/ssb, ssDNA-bd, NA-bd_OB-fold

Expression context

Cohort genes with no expression data: 0.

1 cohort gene are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
calcaneal tendon	1
endometrium	1
islet of Langerhans	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
SSBP1	153	ubiquitous	marker	calcaneal tendon, endometrium, islet of Langerhans

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
SSBP1	4,725

Structural data

PDB: 1 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
SSBP1	Q04837	5

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 7. Enrichment computed across 1 evidence-associated genes (1 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Strand-asynchronous mitochondrial DNA replication	1	1142.0×	0.006	SSBP1
DNA Replication	1	237.9×	0.010	SSBP1
Transcriptional activation of mitochondrial biogenesis	1	203.9×	0.010	SSBP1
Mitochondrial biogenesis	1	167.9×	0.010	SSBP1
Mitochondrial protein degradation	1	114.2×	0.012	SSBP1
Organelle biogenesis and maintenance	1	66.0×	0.018	SSBP1
Metabolism of proteins	1	12.4×	0.081	SSBP1

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
positive regulation of helicase activity	1	8426.0×	3e-04	SSBP1
positive regulation of mitochondrial DNA replication	1	8426.0×	3e-04	SSBP1
mitochondrial DNA replication	1	1532.0×	0.001	SSBP1
protein homotetramerization	1	237.3×	0.005	SSBP1
DNA replication	1	165.2×	0.006	SSBP1

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
SSBP1	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

Symbol	Assays	Type breakdown
SSBP1	1	Binding:1

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	SSBP1

Undrugged target profiles

1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Symbol	ChEMBL assays	Drugged partners (top 3)
SSBP1	1	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.