Meckel syndrome 13

Summary

Meckel syndrome 13 (MONDO:0033044) is a disease caused by TMEM107 (GenCC Strong), with 2 cohort genes.

At a glance

• Causal gene: TMEM107 (GenCC Strong)
• Cohort genes: 2
• ClinVar variants: 11

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	Meckel syndrome 13
Mondo ID	MONDO:0033044
OMIM	617562
DOID	DOID:0080253
UMLS	C4539714
MedGen	1627793
GARD	0016236
Is cancer (heuristic)	no

Also known as: Meckel syndrome 13 · Meckel syndrome, type 13 · MKS13

Data availability: 11 ClinVar variants · 1 GenCC gene-disease record.

Disease family

Classification path: disease › human disease › disease by body system or component › syndromic disease › Meckel syndrome › Meckel syndrome 13

Related subtypes (13): Meckel syndrome, type 1, NPHP3-related Meckel-like syndrome, Meckel syndrome, type 2, Meckel syndrome, type 3, Meckel syndrome, type 4, Meckel syndrome, type 5, Meckel syndrome, type 6, Meckel syndrome, type 8, Meckel syndrome, type 10, Meckel syndrome, type 9, Meckel syndrome, type 11, lethal fetal cerebrorenogenitourinary agenesis/hypoplasia syndrome, meckel syndrome 14

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

11 retrieved; paginated sample, class counts are floors:

4 conflicting classifications of pathogenicity, 3 pathogenic, 1 benign, 1 benign/likely benign, 1 pathogenic/likely pathogenic, 1 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
3362655	NM_183065.4(TMEM107):c.218C>G (p.Ser73Ter)	LOC105371520	Pathogenic	criteria provided, single submitter
430701	NM_183065.4(TMEM107):c.256+1G>A	LOC105371520	Pathogenic	criteria provided, single submitter
430704	NM_183065.4(TMEM107):c.384del (p.Leu128fs)	LOC105371520	Pathogenic	no assertion criteria provided
265788	NM_183065.4(TMEM107):c.*759C>T	SNORD118	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
929273	NR_033294.2(SNORD118):n.82A>G	SNORD118	Likely pathogenic	criteria provided, multiple submitters, no conflicts
872120	NM_183065.4(TMEM107):c.*751C>T	SNORD118	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
929289	NR_033294.2(SNORD118):n.42G>A	SNORD118	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
929293	NR_033294.2(SNORD118):n.8G>A	SNORD118	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
974788	NM_183065.4(TMEM107):c.*609G>A	TMEM107	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1272287	NM_183065.4(TMEM107):c.256+46C>G	LOC105371520	Benign	criteria provided, multiple submitters, no conflicts
1342222	NM_183065.4(TMEM107):c.87+22A>C	LOC105371520	Benign/Likely benign	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · Orphanet: 2 · 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
TMEM107	Strong	Autosomal recessive	Meckel syndrome 13	5

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
TMEM107	Orphanet:564	Meckel syndrome
SNORD118	Orphanet:542310	Leukoencephalopathy with calcifications and cysts

Cohort genes → proteins

2 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	2

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
TMEM107	HGNC:28128	ENSG00000179029	Q6UX40	Transmembrane protein 107	gencc,clinvar
SNORD118	HGNC:32952	ENSG00000200463		small nucleolar RNA, C/D box 118	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
TMEM107	Transmembrane protein 107	Plays a role in cilia formation and embryonic patterning.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 2 · 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	2	1.8×	0.312

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
TMEM107	Other/Unknown	no		TMEM107
SNORD118	Other/Unknown	no

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)	2
unknown	0

Top tissues across cohort

Tissue	Cohort genes
bronchial epithelial cell	1
bronchus	1
right uterine tube	1
adult mammalian kidney	1
kidney	1
sural nerve	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
TMEM107	240	ubiquitous	marker	bronchial epithelial cell, bronchus, right uterine tube
SNORD118	81	ubiquitous	yes	sural nerve, kidney, adult mammalian kidney

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
TMEM107	656
SNORD118	0

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
TMEM107	Q6UX40	94.21

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 2 evidence-associated genes (0 with Reactome annotation).

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
detection of nodal flow	1	5617.3×	0.001	TMEM107
neural tube patterning	1	2808.7×	0.001	TMEM107
protein localization to ciliary transition zone	1	2407.4×	0.001	TMEM107
craniofacial suture morphogenesis	1	1685.2×	0.001	TMEM107
embryonic digit morphogenesis	1	300.9×	0.005	TMEM107
non-motile cilium assembly	1	290.6×	0.005	TMEM107
roof of mouth development	1	247.8×	0.005	TMEM107
regulation of gene expression	1	83.4×	0.013	TMEM107
cilium assembly	1	73.6×	0.014	TMEM107

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 2

Druggability breadth: 0 of 2 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
TMEM107	0	0
SNORD118	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 2; 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	2	TMEM107, SNORD118

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
TMEM107	0	—
SNORD118	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.