c.1103T>C (p.Ile368Th) de novo Variant in Synaptotagmin 1 (SYT1) Gene is Pathogenic, Leading to an Ultra-Rare Neurodevelopmental Disorder: The Baker-Gordon Syndrome

Figures & data

Figure 1 Missense sequence variants of SYT1 deposited in DECIPHER¹³ indicating their location on the protein domains by yellow, Orange, and red dots classified as variant of uncertain significance, Likely pathogenic, and pathogenic respectively. DECIPHER severity tracks related to variant identified in a patient with Baker-Gordon Syndrome from Central Brazil is also included.

Note: This figure makes use of data generated by the DECIPHER community. A full list of centres who contributed to the generation of the data is available from https://deciphergenomics.org/about/stats and via email from [email protected]. DECIPHER is hosted by EMBL-EBI and funding for the DECIPHER project was provided by the Wellcome Trust [grant number WT223718/Z/21/Z].

Figure 2 Phenogram of patients harboring sequence variants in SYT1 (12q21.2). (A) abnormalities by ontological clustering in open access DECIPHER patients;¹³ (B) Synopsis of phenotype of a male patient diagnosed with Baker-Gordon Syndrome from Central Brazil.

Table 1 Patients with BAGOS Phenotype (OMIM #618218), Included in DECIPHER¹³ Until October 2023, Who Exhibited the Syndrome Due to Missense Sequence Variants

Decipher Patient’s ID	Sex	Transcript	Chromosome Location	Consequence	Protein Location	Pathogenicity	Inheritance	Genotype
271292^§	46XY	c.625G>A	12:79296219	p.Glu209Lys	C2A	VUS	de novo	Heterozygous
274395	46XX	c.907A>G	12:79353598	p.Met303Val	C2B	Likely Pathogenic	de novo	Heterozygous
260408	46XX	c.928G>C	12:79353619	p.Asp310His	C2B	Likely Pathogenic	de novo	Heterozygous
306487	46XY	c.935A>G	12:79444079	p.Tyr312Cys	C2B	ni	de novo	Heterozygous
5434541	46XX	c.1016A>G	12:79444160	p.Tyr339Cys	C2B	Likely Pathogenic	de novo^‡	Heterozygous
372118^§	46XY	c.1022A>G	12:79444166	p.Asn341Ser	C2B	ni	de novo^‡	Heterozygous
281640^§	46XY	c.1103T>C	12:79448958	p.Ile368Thr	C2B	Pathogenic	de novo	Heterozygous
422867	46XY	c.1103T>C	12:79448958	p.Ile368Thr	C2B	ni	de novo^‡	Heterozygous
509263^†	46XY	c.1103T>C	12:79448958	p.Ile368Thr	C2B	Pathogenic	de novo	Heterozygous

Notes: ^§Cases formerly reported in Melland et al, 2022; ^†Current patient; ^‡Unconfirmed genotype; Gray shaded rows indicate females; Yellow shaded cells show the most common sequence variant.

Abbreviations: VUS, Variant of Uncertain Significance; ni, not informed.

Firth HV, Richards SM, Bevan AP, et al. DECIPHER: database of chromosomal imbalance and phenotype in humans using ensembl resources. Am J Hum Genet. 2009;84(4):524–533. doi:10.1016/j.ajhg.2009.03.010

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