Submissions for variant NM_016525.5(UBAP1):c.426_427del (p.Lys143fs)

dbSNP: rs1563920252

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Undiagnosed Diseases Network, NIH	RCV000770928	SCV001142586	uncertain significance	Spastic paraplegia 80, autosomal dominant	2019-03-05	criteria provided, single submitter	clinical testing
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	RCV001268741	SCV001447887	pathogenic	not provided	2020-10-23	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV001268741	SCV002063231	pathogenic	not provided	2021-10-01	criteria provided, single submitter	clinical testing
AiLife Diagnostics, AiLife Diagnostics	RCV001268741	SCV002501242	pathogenic	not provided	2020-07-20	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV000770928	SCV003823802	pathogenic	Spastic paraplegia 80, autosomal dominant	2021-11-30	criteria provided, single submitter	clinical testing
Lifecell International Pvt. Ltd	RCV000770928	SCV003926496	pathogenic	Spastic paraplegia 80, autosomal dominant		criteria provided, single submitter	clinical testing	A Heterozygous Frameshift variant c.425_426delAG in Exon 4 of the UBAP1 gene that results in the amino acid substitution p.Lys143fs*15 was identified. The variant was found in ClinVar (Variant ID :627552) with a classification of Pathogenic/Uncertain Significnace and a review status of (1 star) criteria provided, conflicting interpretations. The observed variant has a maximum allele frequency of 0.00% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. The variant has been previously reported in patients with SPG80 (Nan H et al.,2019). Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines.
Baylor Genetics	RCV000770928	SCV004040783	pathogenic	Spastic paraplegia 80, autosomal dominant	2023-03-04	criteria provided, single submitter	clinical testing
OMIM	RCV000770928	SCV000902427	pathogenic	Spastic paraplegia 80, autosomal dominant	2019-05-13	no assertion criteria provided	literature only
The William Harvey Research Institute, Queen Mary University	RCV000770928	SCV001370783	pathogenic	Spastic paraplegia 80, autosomal dominant	2020-05-17	no assertion criteria provided	research