Smpdl3a MGI Mouse Gene Detail - MGI:1931437 - sphingomyelin phosphodiesterase, acid-like 3A

Symbol

Smpdl3a
Name

sphingomyelin phosphodiesterase, acid-like 3A
Synonyms

0610010C24Rik, ASM3A, ASML3A

Feature Type

protein coding gene
IDs

MGI:1931437
NCBI Gene: 57319
Alliance

gene page
Transcription Start Sites

12 TSS

Sequence Map

Chr10:57670640-57687926 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 10, 29.25 cM
Mapping Data

3 experiments

SNPs within 2kb

101 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1931437	protein coding gene	Chr10:57670431-57687926 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0017242	protein coding gene	Chr10:57172740-57197075 (+)
A/J	MGP_AJ_G0017218	protein coding gene	Chr10:55504150-55521553 (+)
AKR/J	MGP_AKRJ_G0017178	protein coding gene	Chr10:56663836-56681384 (+)
BALB/cJ	MGP_BALBcJ_G0017180	protein coding gene	Chr10:55614987-55633471 (+)
C3H/HeJ	MGP_C3HHeJ_G0017002	protein coding gene	Chr10:56892493-56911166 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0017638	protein coding gene	Chr10:58952444-58974010 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0015331	protein coding gene	Chr10:52340922-52360869 (+)
CAST/EiJ	MGP_CASTEiJ_G0016575	protein coding gene	Chr10:56837354-56858413 (+)
CBA/J	MGP_CBAJ_G0016974	protein coding gene	Chr10:61422211-61441543 (+)
DBA/2J	MGP_DBA2J_G0017079	protein coding gene	Chr10:54845384-54863705 (+)
FVB/NJ	MGP_FVBNJ_G0017074	protein coding gene	Chr10:54088835-54108127 (+)
LP/J	MGP_LPJ_G0017154	protein coding gene	Chr10:57273751-57293099 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0017103	protein coding gene	Chr10:63636721-63658570 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0017675	protein coding gene	Chr10:56482857-56500920 (+)
PWK/PhJ	MGP_PWKPhJ_G0016356	protein coding gene	Chr10:54629276-54647073 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0016142	protein coding gene	Chr10:56142982-56162376 (+)
WSB/EiJ	MGP_WSBEiJ_G0016640	protein coding gene	Chr10:56682287-56701896 (+)

Human Ortholog

SMPDL3A, sphingomyelin phosphodiesterase acid like 3A

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SMPDL3A, sphingomyelin phosphodiesterase acid like 3A
Synonyms

ASM3A, ASML3a, yR36GH4.1
Links

HGNC:17389

NCBI Gene ID: 10924

neXtProt AC: NX_Q92484

UniProt: Q92484
Chr Location

6q22.31; chr6:122789049-122809720 (+) GRCh38

MGI Vertebrate Homology

Smpdl3a stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SMPDL3A
Protein SuperFamily

ASM-like_PDE
Gene Tree

Smpdl3a

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Phenotype Summary

2 phenotypes from 1 allele in 1 genetic background
13 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

9
Chemically induced (other)

1
Endonuclease-mediated

5
Radiation induced

1
Targeted

2
Genomic Mutations

2 involving Smpdl3a
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

35 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

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All GO Annotations

15
GO References

7

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

719
Tissues

13
cDNA Data

108
Literature Summary

4

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase smpdl3a

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All Sequences

46
RefSeq

2
UniProt

2
CCDS

CCDS23857.1

Ensembl

ENSMUSG00000019872 (Evidence)
NCBI Gene

57319

			Length	Strain/Species	Flank
genomic	57319	NCBI Gene Model \| MGI Sequence Detail	17287	C57BL/6J	± kb
transcript	NM_020561	RefSeq \| MGI Sequence Detail	1791	C57BL/6
polypeptide	P70158	UniProt \| EBI \| MGI Sequence Detail	445	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000015296 acid sphingomyelinase-like phosphodiesterase 3a

(term hierarchy)
PDB

5FC1, 5FC5, 5FC6, 5FC7, 5FCA, 5FCB
EC

3.1.4.-, 3.6.1.15
InterPro Domains

IPR041805 Acid sphingomyelinase/endopolyphosphatase, metallophosphatase domain

IPR017064 Acid sphingomyelinase-like phosphodiesterase, predicted

IPR004843 Calcineurin-like phosphoesterase domain, ApaH type

IPR029052 Metallo-dependent phosphatase-like

IPR045473 Sphingomyelin phosphodiesterase, C-terminal domain

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All nucleic 109

cDNA 108

Primer pair 1

Microarray probesets 3

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MGI:1917586, MGI:2143639

Summaries

All 48

Developmental Gene Expression 4

Gene Ontology 7

Phenotypes 13
Earliest

J:109968 Roderick TH, et al., Nineteen paracentric chromosomal inversions in mice. Genetics. 1974 Jan;76(1):109-17
Latest

J:342622 Hou Y, et al., SMPDL3A is a cGAMP-degrading enzyme induced by LXR-mediated lipid metabolism to restrict cGAS-STING DNA sensing. Immunity. 2023 Nov 14;56(11):2492-2507.e10

TSS for Smpdl3a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr93409	Chr10:57670466-57670486 (+)	-164 bp
Tssr93410	Chr10:57670623-57670624 (+)	-16 bp
Tssr93411	Chr10:57670644-57670665 (+)	15 bp
Tssr93412	Chr10:57670667-57670760 (+)	74 bp
Tssr93413	Chr10:57670761-57670768 (+)	125 bp
Tssr93414	Chr10:57670779-57670813 (+)	156 bp
Tssr93415	Chr10:57670825-57670846 (+)	196 bp
Tssr93416	Chr10:57677090-57677102 (+)	6,456 bp
Tssr93417	Chr10:57678510-57678528 (+)	7,879 bp
Tssr93418	Chr10:57681700-57681714 (+)	11,067 bp
Tssr93419	Chr10:57683447-57683466 (+)	12,817 bp
Tssr93420	Chr10:57683996-57684029 (+)	13,373 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 04/16/2024 MGI 6.23