1-151612201-G-GAAGGGACATAGTAATTTCCGTTGTTTCATGTTCTAATCTGTATATGGAAGTTTCATTGACAAGCTCATAAAATGGCAGTTCCACACAACTTTGGGAAGCAATAATTTACATTATTAAAATTATCCTGAAA

Variant names:

• chr1-151612201-G-GAAGGGACATAGTAATTTCCGTTGTTTCATGTTCTAATCTGTATATGGAAGTTTCATTGACAAGCTCATAAAATGGCAGTTCCACACAACTTTGGGAAGCAATAATTTACATTATTAAAATTATCCTGAAA
• NM_001330723.2:c.1_2insAGGGACATAGTAATTTCCGTTGTTTCATGTTCTAATCTGTATATGGAAGTTTCATTGACAAGCTCATAAAATGGCAGTTCCACACAACTTTGGGAAGCAATAATTTACATTATTAAAATTATCCTGAAAA

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_Strong PM2

The NM_001330723.2(SNX27):​c.1_2insAGGGACATAGTAATTTCCGTTGTTTCATGTTCTAATCTGTATATGGAAGTTTCATTGACAAGCTCATAAAATGGCAGTTCCACACAACTTTGGGAAGCAATAATTTACATTATTAAAATTATCCTGAAAA​(p.Met1fs) variant causes a frameshift, start lost change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SNX27 NM_001330723.2 frameshift, start_lost
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.70

Genes affected

SNX27 (HGNC:20073): (sorting nexin 27) This gene encodes a member of the sorting nexin family, a diverse group of cytoplasmic and membrane-associated proteins involved in endocytosis of plasma membrane receptors and protein trafficking through these compartments. All members of this protein family contain a phosphoinositide binding domain (PX domain). A highly similar protein in mouse is responsible for the specific recruitment of an isoform of serotonin 5-hydroxytryptamine 4 receptor into early endosomes, suggesting the analogous role for the human protein. [provided by RefSeq, Jul 2008]

ENSG00000250734 (HGNC:):

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 14 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX27	NM_001330723.2	c.1_2insAGGGACATAGTAATTTCCGTTGTTTCATGTTCTAATCTGTATATGGAAGTTTCATTGACAAGCTCATAAAATGGCAGTTCCACACAACTTTGGGAAGCAATAATTTACATTATTAAAATTATCCTGAAAA	p.Met1fs	frameshift_variant, start_lost	Exon 1 of 12	ENST00000458013.7	NP_001317652.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX27	ENST00000458013.7	c.1_2insAGGGACATAGTAATTTCCGTTGTTTCATGTTCTAATCTGTATATGGAAGTTTCATTGACAAGCTCATAAAATGGCAGTTCCACACAACTTTGGGAAGCAATAATTTACATTATTAAAATTATCCTGAAAA	p.Met1fs	frameshift_variant, start_lost	Exon 1 of 12	5	NM_001330723.2	ENSP00000400333.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Severe myoclonic epilepsy in infancy Uncertain:1

Jun 29, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with SNX27-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change affects the initiator methionine of the SNX27 mRNA. The next in-frame methionine is located at codon 187. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-151584677;