Expanding the Variant Spectrum of MED13L-Associated Neurodevelopmental Disorder: Insights from the 100k Genomes Project

Introduction

Data and Methods Section

Characterization of Probands

Detailed clinical profiles were compiled for all probands carrying filtered MED13L variants. Features were compared between those with likely pathogenic variants and those with variants of uncertain significance. A comprehensive literature review was conducted to confirm the novelty of each variant.

Through this approach, nine probands with rare MED13L variants were identified and characterized, contributing to the broader understanding of the gene’s role in neurodevelopmental disorders (see Figure 1).

Figure 1. Variant filtering steps and number of variants after each filtering step.

Figure 1. Variant filtering steps and number of variants after each filtering step.

Figure 2. Demographic information across all Genomics England Projects: Self defined ethnicity [11].

Figure 2. Demographic information across all Genomics England Projects: Self defined ethnicity [11].

Figure 3. Demographic information across all Genomics England Projects: Chromosomal Sex [11].

Figure 3. Demographic information across all Genomics England Projects: Chromosomal Sex [11].

Figure 4. A Demographic information across all Genomics England Projects: Year of birth (taken from Genomics England Public Data Browser) [11].

Figure 4. A Demographic information across all Genomics England Projects: Year of birth (taken from Genomics England Public Data Browser) [11].

Figure 5. Types of rare diseases in the 100k Genomes rare disease group (taken from Genomics England Public Data Browser) [12].

Figure 5. Types of rare diseases in the 100k Genomes rare disease group (taken from Genomics England Public Data Browser) [12].

Figure 6. Overview of disorders of psychological development (F80-F89) in the 100k Genomes rare disease cohort [13].

Figure 6. Overview of disorders of psychological development (F80-F89) in the 100k Genomes rare disease cohort [13].

Results (The following results refer to various databases as of 18th March 2026)

Discussion

Clinical Implications of Findings

Genetic heterogeneity—defined as pathogenic variants in different genes or alleles producing similar clinical phenotypes—emerged as a recurring feature within this cohort. In four of the eight probands, additional pathogenic or likely pathogenic variants were identified in genes distinct from MED13L, including ASXL3, IQSEC2, and COQ4. These genes are independently associated with neurodevelopmental disorders that may clinically overlap with MED13L-related syndromes. The presence of multiple pathogenic variants in individual probands raises the possibility of multilocus contributions to the observed phenotypes.

To date, most studies focused specifically on MED13L syndrome have not reported comparable levels of genetic heterogeneity.[7,8,16] A notable exception is the study by Mullegama et al., which described a patient harboring pathogenic variants in both DEAF1 and MED13L. Following in vitro functional analyses and comprehensive phenotypic evaluation, the authors concluded that the clinical presentation was most consistent with MED13L haploinsufficiency syndrome. [17]

The discrepancy between prior reports and the present findings may reflect differences in study design and cohort ascertainment. The Genomics England dataset, from which several participants in this study were drawn, recruits broadly across rare diseases rather than exclusively targeting neurodevelopmental phenotypes. Moreover, all participants undergo whole-genome sequencing, rather than phenotype-driven targeted gene panel sequencing, thereby enabling the detection of pathogenic variants beyond those initially suspected based on clinical presentation. Such an approach may increase the likelihood of detecting co-occurring pathogenic variants and capturing a more genetically heterogeneous population.

More broadly, emerging evidence in neurodevelopmental disorders supports the concept of cumulative genetic burden. A recent case study described a patient carrying heterozygous variants in HDAC8 and genes within the FA/BRCA pathway, suggesting a potential combined effect on disease expression.[18] Similarly, oligogenic models are increasingly considered in autism spectrum disorder, where multiple rare variants may contribute additively or interactively to phenotypic manifestation. [19,20]

Case Studies of Genetic Heterogeneity

Patient 3 was diagnosed with Bainbridge-Ropers syndrome (#OMIM 615485) due to a pathogenic nonsense variant in ASXL3 (chromosome 18: position: 33746183, c.6335 T>A; p.Leu2112Ter), causing a stop mutation alongside a VUS in MED13L. Bainbridge-Ropers syndrome (BRPS) presents with clinical features overlapping MED13L syndrome, including severe intellectual disability, delayed psychomotor development, hypotonia, feeding difficulties, growth impairment, and dysmorphic facial characteristics.[21]

Patient 5, a female proband, harbored multiple pathogenic or likely pathogenic variants, including alterations in IQSEC2 and MED13L. Genomic analysis identified a TG/T deletion at chromosomal position X:53320894 within IQSEC2 (UniProt accession AC245102). [22] This deletion results in a frameshift predicted to produce a truncated or functionally compromised protein and was classified as pathogenic by Genomics England.

Pathogenic variants in IQSEC2 are typically associated with severe intellectual disability, hypotonia, strabismus, stereotypic behaviors, autism spectrum disorder, postnatal microcephaly, and epilepsy. [23]

As IQSEC2-related disorders follow an X-linked dominant inheritance pattern, [23] affected females are frequently less severely impacted than males. This sex difference is attributed to X-chromosome inactivation (XCI), whereby heterozygous females exhibit mosaic expression of mutant and wild-type alleles. Depending on the degree of XCI skewing, this mosaicism can lead to a milder or more variable phenotype. Consistent with this mechanism, Kalscheuer et al. (2016) reported attenuated clinical manifestations in female carriers within affected pedigrees. [24]

The proband exhibited several features consistent with IQSEC2-related neurodevelopmental disorder, particularly intellectual disability and hypotonia. However, in contrast to the classical presentation, no recurrent or unprovoked seizures were reported; seizure activity was limited to febrile convulsions. Given that epilepsy is a common and often prominent feature of IQSEC2-associated disease, the absence of epilepsy in this patient suggests a comparatively attenuated phenotypic presentation, in line with the literature on female patients. However, the relative contribution of each gene to the overall clinical presentation remains uncertain.

Notably, RPSAP62, also identified in this proband, has no established disease association in OMIM and is likely an incidental finding.

In addition to a likely pathogenic MED13L mutation, patient 6 harbored a pathogenic variant in COQ4 as well as a variant in TRUB2. While TRUB2 is not known to be associated with any disease and likely incidental, COQ4 is implicated in pathogenicity. Notably, TRUB2 and COQ4 are located in close genomic proximity. Complex structural variations such as a deletion-insertion-duplication event could potentially encompass these two loci, representing a larger genomic rearrangement (see Figure 8).

Mutations in COQ4 have been linked to primary coenzyme Q10 deficiency, a condition with a clinically heterogeneous presentation. While most cases exhibit variable neurological symptoms, Brea-Calvo et al. reported a patient with COQ4-related disease who exhibited a progressive course of neurological deterioration.[25] Given the broad neurodevelopmental phenotype observed in this patient, it is evident that the proband presents with a dual diagnosis of MED13L syndrome and primary coenzyme Q10 deficiency, highlighting the complexity of the underlying genetic etiology.

Patient 7 – This patient was initially diagnosed by Genomics England with a likely pathogenic variant in the MED13L gene, a finding that was subsequently confirmed in the present study. In addition to this pathogenic variant, the patient has been assigned a diagnosis of chromosomal abnormality, classified under the ICD-10 code for chromosomal disorders. However, the clinical significance of this chromosomal abnormality remains uncertain, and it is unclear whether it contributes to the patient’s neurodevelopmental phenotype.

The present result corroborates previous findings from Genomics England, thereby replicating and reinforcing established genotype–phenotype associations.

Table 3. Patient types identified by the present study and their implications as well as recommendations.

Table 3. Patient types identified by the present study and their implications as well as recommendations.

Patient Number	Variant classification	Additional Comments	Patient type	Implication	Recommendations For a diagnostic lab
Patient 1	VUS in MED13L, no other variants		VUS		Consider further action: Additional tests/investigations (trio sequencing) could re-classify the VUS as likely pathogenic
Patient 2	VUS in MED13L, no other variants		VUS		Consider further action: Additional tests/investigations (trio sequencing) could re-classify the VUS as likely pathogenic
Patient 3	VUS in MED13L and asxl3 (pathogenic variant)		VUS and pathogenic variant-VUS		Consider further action: Additional tests/investigations (trio sequencing) could re-classify the VUS as likely path.
Patient 4	VUS in MED13L, no other variants	Heart: other congenital malformations of aorta (Q25.4), cardiac phenotype	VUS
Patient 5	Likely pathogenic in MED13L, Also variants in RPSAP62, IQSEQ2: AC245102 (accession number)	Mild phenotype	Pathogenic and Likely Pathogenic	2 disease causing variants at the same time	Report to Genomics England about likely pathogenic variant newly found by the present study, to pass on information to the clinician
Patient 6	Primary coenzyme q10 deficiency, and likely pathogenic in VUS, variants in COQ4 and TRUB2	bradycardia	Pathogenic and Likely Pathogenic	2 disease causing variants at the same time	Report to Genomics England about likely pathogenic variant newly found by the present study, to pass on information to the clinicain
Patient 7	Pathogenic in MED13L, chromosomal abnormality		Pathogenic	Replication (as already reported by Genomics England)	Consider further action: Additional tests/investigations (trio sequencing) could re-classify the VUS as likely path.
Patient 8	VUS in MED13L (confirmed by Genomics England), no other variants		VUS	Replication (as already reported by Genomics England)	Consider further action: Additional tests/investigations (trio sequencing) could re-classify the VUS as likely path.
Patient 9	VUS in MED13L , no other variants		VUS	Replication (as already reported by Genomics England)	Consider further action: Additional tests/investigations (trio sequencing) could re-classify the VUS as likely path.

Conclusion

Further Research

The study’s findings advocate for continued research and clinical focus on comprehensive genetic evaluations that leverage diverse, large-scale data for more inclusive and precise medical insights.

A complex relationship between MED13L mutations and cardiac phenotypes is suggested. In particular, the mechanisms and phenotypic consequences of intronic MED13L variants remain poorly understood. Additional data from MED13L carriers are necessary to refine the estimated penetrance of cardiac phenotypes.

Consistent with Chen et al.[27], these findings underscore the importance of increasing ethnic diversity in genomic databases and improving methods to evaluate missense variants—especially those classified as VUS. Integrating clinical and experimental data, including functional studies, will be crucial for reducing uncertainty in variant interpretation.

Reclassification of VUS remains a challenge. Pathogenicity can often only be confirmed when similar cases are reported with matching phenotypes. Functional validation studies are essential to assess the impact of these variants.

This study also highlights the need for comprehensive genomic analysis to examine the role of MED13L within broader neurodevelopmental risk architectures. Deep phenotyping is necessary to better understand the clinical implications of such co-occurring mutations, and functional studies on the variants of uncertain significance found, should be carried out.

Intronic MED13L variants remain under-characterized. Muncke et al.[5] identified a total of four missense and six intronic mutations in their cohort, noting that although intronic and synonymous variants cannot be categorically dismissed—particularly when absent from control populations—they did not undertake a detailed functional assessment of the intronic alterations. This gap in knowledge emphasizes the need for comprehensive studies that examine the contribution of non-coding variants to structural and anatomical abnormalities.

Future work should also explore age-related factors, cancer prevalence, and broaden the known phenotypic spectrum associated with MED13L variants.

Table 4. Overview of numbers after filtering steps of MED13L gene variants from the 100k Genomes Project GRCh38 Germline Programme (Rare Disease Programme).

Table 4. Overview of numbers after filtering steps of MED13L gene variants from the 100k Genomes Project GRCh38 Germline Programme (Rare Disease Programme).

Type of variants	Absolute numbers	Number of participants	Percentage of variants
Total number of variants affecting MED13L (all types of coding and non-coding variants) (from 100k Genomes Project GRCh38 Germline programme - rare disease programme, March 2025)	66937 variants observed in the IVA rare disease programme	63349 participants	100%
Number of variants with MAF <0.01 (less than 1%) (from GnomAD) (from 100k Genomes Project GRCh38 Germline programme - rare disease programme)	65857 variants		98.387%
Number of variants that are truncating (frame shift, stop gained, splice acceptor and splice donor variants, Indel (less 50bp) and SNV) (from 100k Genomes Project IVA rare disease GRCh38 cohort ) – without applying MAF	57 variants	268 probands	0.085%
Number of missense/inframe variants (from 100k Genomes Project GRCh38 Germline programme - rare disease programme)	438 variants (when filtering for MAF <0.01, it is 438 variants as well)	1530 probands	0.654%
Number of variants left after including variants unreported in GnomAD (from GnomAD)	91 variants	--	0.136%
Number of variants after excluding people who did not fit phenotype (with no neurodevelopmental feature) or families where several members had same MED13L variant but different phenotypes (from 100k Genomes Project GRCh38 Germline programme - rare disease programme)	7 variants	7 probands	0.01%
Number of VUS (from 100k Genomes Project GRCh38 Germline programme - rare disease programme)	3 variants	3 probands	0.01%

Table 5. Variant classification based on criteria by the American College of Medical Genetics and Genomics [28].

Table 5. Variant classification based on criteria by the American College of Medical Genetics and Genomics [28].

Patient	C.nomenclature/ p.nomenclature	Absent from database (reported in GnomAD)	Absent from database (reported in ClinVar on 21st Jan 2025)	NGS analysis carried out	Computational evidence (in silico predictions CADD, SIFT, Polyphen, AlphaMissense)	SIFT	Polyphen	CADD	Alphamissense (with score)	Published in the literature	Final classification
Patient 1	c.250T>C/ p.TRP84ARG	No	No	Duo (absent in mother or father)	3 pathogenic lines of evidence	Deleterious (0)	0 (unknown)	25/4.339121	Likely pathogenic (0.9988)	No	VUS
Patient 2	c.2432A>G/ p.ASP811GLY	No	No	Duo (absent in mother or father)	2 pathogenic lines of evidence	Deleterious (0)	Unknown (0)	29.2	0.4252778 (ambiguous)	No	VUS
Patient 3	c.4745C>A/p.SER1582TYR	No	No	Duo (absent in mother or father)	2 pathogenic lines of evidence	Deleterious(0)	Unknown (0)	23.4	0.1857(likely benign)	No	VUS (leans towards benign, as patient has other disease causing mutation (ASXL3))
Patient 4	Intronic variant	No	No	Duo (absent in mother or father)	2 pathogenic lines of evidence	Intronic isoform	MaxEntScandiff -0.234	MaxEntScanAlt 8.680		No	VUS
						missense isoform 0.04 (tolerated low confidence)	0.001	0.139432 (RawScore), 1.823 (PHRED score) (https://cadd.gs.washington.edu/snv) -benign	Not available
Patient 5	c.1466A>G/p.HIS489ARG	No	No	Trio	2 pathogenic lines of evidence	Deleterious (0)	Unknown (0)	22.2	Ambiguous (0.4852)	No	Likely Pathogenic
Patient 6	c.1688C>A/p. p.PRO563GLN	No	No	Trio	2 pathogenic lines of evidence	Deleterious (0)	Unknown (0)	26.5	Ambiguous (0.4309)	No	Likely Pathogenic
Patient 7	c.2614G>A/ p. GLU872LYS	No	No	Trio- on GEL de novo list	3 pathogenic lines of evidence	Deleterious (0)	0	27.6	Likely pathogenic (0.9851)	No	Likely Pathogenic (classified likely path. in GEL)
Patient 8	c.3481_3486/p.Thr1161_Cys1162	No	No	Duo	Not available as inframe deletion					No	VUS
Patient 9	c.5870G>C/ p.Gly1957Val	No	No	Singleton	2 pathogenic lines of evidence	Benign (0.06)	Pathogenic (0.999)	Pathogenic (26.2)	Benign (0.1789)	No	VUS

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