NM_015087.5:c.*2127_*2130dupGATA

Variant names:

• chr13-36302234-T-TTATC
• rs150662490
• NM_015087.5:c.*2127_*2130dupGATA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_015087.5(SPART):​c.*2127_*2130dupGATA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 24)
• Consequence: SPART NM_015087.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPART	NM_015087.5	c.*2127_*2130dupGATA		3_prime_UTR_variant	Exon 9 of 9	ENST00000438666.7	NP_055902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPART	ENST00000438666	c.*2127_*2130dupGATA		3_prime_UTR_variant	Exon 9 of 9	1	NM_015087.5	ENSP00000406061.2
SPART	ENST00000451493	c.*2127_*2130dupGATA		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000414147.1
SPART	ENST00000355182	c.*2127_*2130dupGATA		3_prime_UTR_variant	Exon 9 of 9	5		ENSP00000347314.4
SPART	ENST00000650221	c.*2127_*2130dupGATA		3_prime_UTR_variant	Exon 10 of 10			ENSP00000497209.1

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs150662490; hg19: chr13-36876371;