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Varaico: Literature-Extracted Genetic Variants

Include likely false extractions

Gene:SMPD2

SMPD2

60 papers

RefSeq Summary

This gene encodes a protein which was initially identified as a sphingomyelinase based on sequence similarity between bacterial sphingomyelinases and a yeast protein. Subsequent studies showed that it...

Pfam Domains

Exo_endo_phosaa 12–272UCSCEndonuclease/Exonuclease/phosphatase family

Gene Aliases

HGNC Name

sphingomyelin phosphodiesterase 2

HGNC Alias Symbols

nSMase; ISC1

Papers

Position

RefSeq ID

Protein change

DNA change

Pfam

gnomAD

1–12 of 57 variants

5 papers

chr6:109443332 G>C

NM_003080.3

p.R265S

c.795G>C

Exo_endo_phos

exact variant not in gnomAD83 overlapping SVs

5 papers

chr6:109443332 G>T

NM_003080.3

p.R265S

c.795G>T

Exo_endo_phos

Exome: 43.5% (AC=636030, hom=141539)Genome: 51.5% (AC=78322, hom=21333)83 overlapping SVs

3 papers

chr6:109441129 C>T

NM_003080.3

p.P3L

c.8C>T

Exome: 4.9% (AC=72251, hom=3171)Genome: 6.0% (AC=9196, hom=410)84 overlapping SVs

2 papers

chr6:109443019 G>A

NM_003080.3

p.V223I

c.667G>A

Exo_endo_phos

Exome: 0.1% (AC=1365, hom=23)Genome: 0.1% (AC=206, hom=5)83 overlapping SVs

1 paper

chr6:109441144 G>A

NM_003080.3

p.R8Q

c.23G>A

Exome: 0.0% (AC=3, hom=0)Genome: 0.0% (AC=1, hom=0)84 overlapping SVs

1 paper

chr6:109441149 C>T

NM_003080.3

p.R10W

c.28C>T

exact variant not in gnomAD84 overlapping SVs

1 paper

chr6:109441150 G>T

NM_003080.3

p.R10L

c.29G>T

Exome: 0.0% (AC=0, hom=0)Genome: n/a84 overlapping SVs

1 paper

chr6:109441427 A>C

NM_003080.3

p.S41R

c.121A>C

Exo_endo_phos

Exome: 0.0% (AC=6, hom=0)Genome: n/a83 overlapping SVs

1 paper

chr6:109441429 C>A

NM_003080.3

p.S41R

c.123C>A

Exo_endo_phos

exact variant not in gnomAD83 overlapping SVs

1 paper

chr6:109441429 C>G

NM_003080.3

p.S41R

c.123C>G

Exo_endo_phos

exact variant not in gnomAD83 overlapping SVs

1 paper

chr6:109441450 G>A

NM_003080.3

p.E48E

c.144G>A

Exo_endo_phos

exact variant not in gnomAD83 overlapping SVs

1 paper

chr6:109441451 G>C

NM_003080.3

p.E49Q

c.145G>C

Exo_endo_phos

exact variant not in gnomAD83 overlapping SVs

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Regarding the variants extracted from papers and shown text snippets from research papers, the following holds: "Some rights reserved. This work permits non-commercial use, distribution and reproduction in any medium, provided the original author and source are credited."