rs878854993

Variant names:

• chr13-36329473-A-G
• rs878854993
• NM_015087.5:c.1053T>C

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_015087.5(SPART):​c.1053T>C​(p.Pro351Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: SPART NM_015087.5 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.72
• Publications: 0 publications found

Genes affected

SPART (HGNC:18514): (spartin) This gene encodes a protein containing a MIT (Microtubule Interacting and Trafficking molecule) domain, and is implicated in regulating endosomal trafficking and mitochondria function. The protein localizes to mitochondria and partially co-localizes with microtubules. Stimulation with epidermal growth factor (EGF) results in protein translocation to the plasma membrane, and the protein functions in the degradation and intracellular trafficking of EGF receptor. Multiple alternatively spliced variants, encoding the same protein, have been identified. Mutations associated with this gene cause autosomal recessive spastic paraplegia 20 (Troyer syndrome). [provided by RefSeq, Nov 2008]

SPART Gene-Disease associations (from GenCC):

• Troyer syndrome

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BP6: Variant 13-36329473-A-G is Benign according to our data. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr13-36329473-A-G is described in CliVar as Likely_benign. Clinvar id is 240961.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=1.72 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPART	NM_015087.5	c.1053T>C	p.Pro351Pro	synonymous_variant	Exon 4 of 9	ENST00000438666.7	NP_055902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPART	ENST00000438666.7	c.1053T>C	p.Pro351Pro	synonymous_variant	Exon 4 of 9	1	NM_015087.5	ENSP00000406061.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Apr 06, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	8.9
DANN	Benign	0.76
PhyloP100		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs878854993; hg19: chr13-36903610;