5-151467262-T-TCTGG

Variant names:

• chr5-151467262-T-TCTGG
• rs755546492
• NM_078483.4:c.487_490dupGCTG

Variant summary

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

The NM_078483.4(SLC36A1):​c.487_490dupGCTG​(p.Asp164GlyfsTer2) variant causes a frameshift, stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000617 in 1,458,514 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0000062 (0 hom.)
• Consequence: SLC36A1 NM_078483.4 frameshift, stop_gained
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 2.96

Genes affected

SLC36A1 (HGNC:18761): (solute carrier family 36 member 1) This gene encodes a member of the eukaryote-specific amino acid/auxin permease (AAAP) 1 transporter family. The encoded protein functions as a proton-dependent, small amino acid transporter. This gene is clustered with related family members on chromosome 5q33.1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

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
SLC36A1	NM_078483.4	c.487_490dupGCTG	p.Asp164GlyfsTer2	frameshift_variant, stop_gained	Exon 6 of 11	ENST00000243389.8	NP_510968.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC36A1	ENST00000243389.8	c.487_490dupGCTG	p.Asp164GlyfsTer2	frameshift_variant, stop_gained	Exon 6 of 11	1	NM_078483.4	ENSP00000243389.3
SLC36A1	ENST00000521925.5	c.487_490dupGCTG	p.Asp164GlyfsTer2	frameshift_variant, stop_gained	Exon 6 of 10	1		ENSP00000430305.1
SLC36A1	ENST00000429484.6	c.487_490dupGCTG	p.Asp164GlyfsTer2	frameshift_variant, stop_gained	Exon 6 of 9	1		ENSP00000395640.2
SLC36A1	ENST00000520701.5	c.487_490dupGCTG	p.Asp164GlyfsTer2	frameshift_variant, stop_gained	Exon 6 of 11	5		ENSP00000428140.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD3 exomes AF: 0.00000801 AC: 2 AN: 249706 Hom.: 0 AF XY: 0.0000148 AC XY: 2 AN XY: 135030

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000660

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000617 AC: 9 AN: 1458514 Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8 AN XY: 725796

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000105

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 30

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Autism Uncertain:1

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Centre for Addiction & Mental Health, Centre for Addiction & Mental Health

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

Gene not previously associated with disease; independent supporting evidence needed -

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: rs755546492; hg19: chr5-150846823;