Seckel syndrome 8

Summary

Seckel syndrome 8 (MONDO:0014350) is a disease caused by DNA2 (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: DNA2 (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 17

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	Seckel syndrome 8
Mondo ID	MONDO:0014350
OMIM	615807
DOID	DOID:0070009
UMLS	C3891452
MedGen	856014
GARD	0016013
Is cancer (heuristic)	no

Also known as: DNA2 Seckel syndrome · SCKL8 · Seckel syndrome 8 · Seckel syndrome caused by mutation in DNA2 · Seckel syndrome type 8

Data availability: 17 ClinVar variants · 4 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › syndromic disease › Seckel syndrome › Seckel syndrome 8

Related subtypes (11): Seckel syndrome 1, intrauterine growth retardation with increased mitomycin c sensitivity, Seckel syndrome 2, Seckel syndrome 4, Seckel syndrome 5, Seckel syndrome 6, Seckel syndrome 7, microcephaly 13, primary, autosomal recessive, Seckel syndrome 9, Seckel syndrome 10, Seckel syndrome 11

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

17 retrieved; paginated sample, class counts are floors:

5 benign/likely benign, 3 uncertain significance, 3 benign, 2 pathogenic, 2 conflicting classifications of pathogenicity, 1 pathogenic/likely pathogenic, 1 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
143932	NM_001080449.3(DNA2):c.3114+6del	DNA2	Pathogenic/Likely pathogenic	no assertion criteria provided
3235127	NM_001080449.3:c.1764-38_1764-37insGAACCTCAAACAGCCAGGAGCAGCTGGAATGCAGGCCTTTCACTCCACTTTTC	DNA2	Pathogenic	no assertion criteria provided
3235129	NM_001080449.3(DNA2):c.1963A>G (p.Thr655Ala)	DNA2	Pathogenic	no assertion criteria provided
2907397	NM_001080449.3(DNA2):c.74+4A>C	DNA2	Likely pathogenic	criteria provided, single submitter
3650985	NM_001080449.3(DNA2):c.1871del (p.Lys624fs)	DNA2	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
41477	NM_001080449.3(DNA2):c.593G>A (p.Arg198His)	DNA2	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1031788	NM_001080449.3(DNA2):c.707T>C (p.Met236Thr)	DNA2	Uncertain significance	criteria provided, single submitter
1033659	NM_001080449.3(DNA2):c.2156G>T (p.Arg719Ile)	DNA2	Uncertain significance	criteria provided, single submitter
1333688	NM_001080449.3(DNA2):c.916A>T (p.Asn306Tyr)	DNA2	Uncertain significance	criteria provided, multiple submitters, no conflicts
257343	NM_001080449.3(DNA2):c.2430C>G (p.Phe810Leu)	DNA2	Benign/Likely benign	criteria provided, multiple submitters, no conflicts
257346	NM_001080449.3(DNA2):c.507C>A (p.Ala169=)	DNA2	Benign	criteria provided, multiple submitters, no conflicts
381847	NM_001080449.3(DNA2):c.888G>A (p.Pro296=)	DNA2	Benign/Likely benign	criteria provided, multiple submitters, no conflicts
382984	NM_001080449.3(DNA2):c.295T>C (p.Leu99=)	DNA2	Benign/Likely benign	criteria provided, multiple submitters, no conflicts
385006	NM_001080449.3(DNA2):c.1649A>G (p.Asn550Ser)	DNA2	Benign/Likely benign	criteria provided, multiple submitters, no conflicts
429200	NM_001080449.3(DNA2):c.2697+13del	DNA2	Benign	criteria provided, multiple submitters, no conflicts
516414	NM_001080449.3(DNA2):c.1057+19del	DNA2	Benign	criteria provided, multiple submitters, no conflicts
559218	NM_001080449.3(DNA2):c.720-4del	DNA2	Benign/Likely benign	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 9 · Orphanet: 3 · 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
DNA2	Strong	Autosomal recessive	Seckel syndrome 8	9

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
DNA2	Orphanet:352470	DNA2-related mitochondrial DNA deletion syndrome
DNA2	Orphanet:715635	Rothmund-Thomson syndrome type 4
DNA2	Orphanet:808	Seckel syndrome

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
DNA2	HGNC:2939	ENSG00000138346	P51530	DNA replication ATP-dependent helicase/nuclease DNA2	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
DNA2	DNA replication ATP-dependent helicase/nuclease DNA2	Key enzyme involved in DNA replication and DNA repair in nucleus and mitochondrion.

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)
DNA2	Other/Unknown	no		PDDEXK-like_dom_sf, DNA_replication_fac_Dna2_N, Dna2/JHS1_DEXXQ-box

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
Brodmann (1909) area 10	1
primordial germ cell in gonad	1
secondary oocyte	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
DNA2	192	ubiquitous	marker	secondary oocyte, primordial germ cell in gonad, Brodmann (1909) area 10

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
DNA2	2,792

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
DNA2	P51530	1

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 16. 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
Removal of the Flap Intermediate	1	815.7×	0.005	DNA2
Removal of the Flap Intermediate from the C-strand	1	634.4×	0.005	DNA2
Impaired BRCA2 binding to PALB2	1	456.8×	0.005	DNA2
Defective homologous recombination repair (HRR) due to BRCA1 loss of function	1	423.0×	0.005	DNA2
Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function	1	423.0×	0.005	DNA2
Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function	1	423.0×	0.005	DNA2
Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)	1	393.8×	0.005	DNA2
Homologous DNA Pairing and Strand Exchange	1	380.7×	0.005	DNA2
Impaired BRCA2 binding to RAD51	1	308.6×	0.005	DNA2
Resolution of D-loop Structures through Holliday Junction Intermediates	1	300.5×	0.005	DNA2
HDR through Single Strand Annealing (SSA)	1	292.8×	0.005	DNA2
Presynaptic phase of homologous DNA pairing and strand exchange	1	271.9×	0.005	DNA2
HDR through Homologous Recombination (HRR)	1	190.3×	0.006	DNA2
G2/M DNA damage checkpoint	1	120.2×	0.009	DNA2
Regulation of TP53 Activity through Phosphorylation	1	117.7×	0.009	DNA2
Processing of DNA double-strand break ends	1	114.2×	0.009	DNA2

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
DNA replication, Okazaki fragment processing	1	16852.0×	9e-04	DNA2
mitotic telomere maintenance via semi-conservative replication	1	5617.3×	0.001	DNA2
DNA replication, removal of RNA primer	1	4213.0×	0.001	DNA2
replication fork reversal	1	3370.4×	0.001	DNA2
telomere maintenance via semi-conservative replication	1	2808.7×	0.001	DNA2
mitochondrial DNA repair	1	2407.4×	0.001	DNA2
DNA geometric change	1	2106.5×	0.001	DNA2
DNA double-strand break processing	1	1532.0×	0.001	DNA2
mitochondrial DNA replication	1	1532.0×	0.001	DNA2
t-circle formation	1	1404.3×	0.001	DNA2
DNA replication checkpoint signaling	1	1296.3×	0.001	DNA2
positive regulation of DNA replication	1	581.1×	0.002	DNA2
base-excision repair	1	468.1×	0.002	DNA2
telomere maintenance	1	267.5×	0.004	DNA2
DNA replication	1	165.2×	0.006	DNA2

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
DNA2	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
DNA2	23	Binding:23

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	DNA2

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)
DNA2	23	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.