Submissions for variant NM_015087.5(SPART):c.364_365del (p.Met122fs)

gnomAD frequency: 0.00009  dbSNP: rs775736341

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000624566	SCV000740970	pathogenic	Inborn genetic diseases	2015-07-10	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV001090324	SCV001245810	pathogenic	not provided	2017-10-01	criteria provided, single submitter	clinical testing
Institute of Human Genetics, University of Leipzig Medical Center	RCV000003622	SCV001443052	pathogenic	Troyer syndrome	2020-03-01	criteria provided, single submitter	clinical testing	Review of the variants reported in Reuter et al., 2017, PMID: 28097321: PVS1,PM2,PM3,PP1_Strong
Labcorp Genetics (formerly Invitae), Labcorp	RCV001090324	SCV001583149	pathogenic	not provided	2024-11-30	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal (p.Met122Valfs*2) in the SPART gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SPART are known to be pathogenic (PMID: 18413476, 20437587, 20504295). This variant is present in population databases (rs775736341, gnomAD 0.02%). This premature translational stop signal has been observed in individuals with Troyer syndrome (PMID: 20437587, 26003402, 27112432). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 3458). For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity	RCV000003622	SCV002021913	pathogenic	Troyer syndrome	2021-07-30	criteria provided, single submitter	clinical testing
GeneDx	RCV001090324	SCV002525278	pathogenic	not provided	2023-12-14	criteria provided, single submitter	clinical testing	Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 27112432, 28679690, 28875386, 20437587, 28097321, 26003402, 34396080, 27535533)
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille	RCV002273920	SCV002559074	pathogenic	Neurodevelopmental delay		criteria provided, single submitter	clinical testing
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre	RCV001090324	SCV005438456	pathogenic	not provided	2024-12-18	criteria provided, single submitter	clinical testing
OMIM	RCV000003622	SCV000023785	pathogenic	Troyer syndrome	2010-04-01	no assertion criteria provided	literature only
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University	RCV000003622	SCV000891557	pathogenic	Troyer syndrome	2017-12-30	no assertion criteria provided	curation
New York Genome Center	RCV000003622	SCV002097741	uncertain significance	Troyer syndrome	2021-01-13	flagged submission	clinical testing