SACM1L SAC1 like phosphatidylinositide phosphatase [Homo sapiens (human)] - Gene

Summary

Official Symbol: SACM1Lprovided by HGNC
Official Full Name: SAC1 like phosphatidylinositide phosphataseprovided by HGNC
Primary source: HGNC:HGNC:17059
See related: Ensembl:ENSG00000211456 MIM:606569; AllianceGenome:HGNC:17059
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SAC1
Summary: This gene encodes an integral membrane protein, which is localized to the endoplasmic reticulum, and functions as a phosphoinositide phosphatase that hydrolyzes phosphatidylinositol 3-phosphate, phosphatidylinositol 4-phosphate, and phosphatidylinositol 3,5-bisphosphate. Deletion of this gene in mouse results in preimplantation lethality. Other studies suggest that this gene is also involved in the organization of golgi membranes and mitotic spindles. Alternatively spliced transcript variants have been found for this gene. A C-terminally extended isoform is also predicted to be produced by the use of an alternative in-frame, downstream translation termination codon via a stop codon readthrough mechanism.[provided by RefSeq, Dec 2017]
Expression: Ubiquitous expression in thyroid (RPKM 28.5), lung (RPKM 17.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p21.31

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (45689396..45745409)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (45705375..45761083)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (45730888..45786901)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Sac1 phosphatidylinositol 4-phosphate phosphatase is a novel host cell factor regulating hepatitis B virus particles assembly and release.
Title: Sac1 phosphatidylinositol 4-phosphate phosphatase is a novel host cell factor regulating hepatitis B virus particles assembly and release.
The activity of Sac1 across ER-TGN contact sites requires the four-phosphate-adaptor-protein-1.
Title: The activity of Sac1 across ER-TGN contact sites requires the four-phosphate-adaptor-protein-1.
the component proteins of the machinery, OSBP, VAP, SAC1, and PITPNB, are all essential host factors for AiV replication. Importantly, the machinery is directly recruited to the RNA replication sites through previously unknown interactions of VAP/OSBP/SAC1 with the AiV proteins and with ACBD3.
Title: Model of OSBP-Mediated Cholesterol Supply to Aichi Virus RNA Replication Sites Involving Protein-Protein Interactions among Viral Proteins, ACBD3, OSBP, VAP-A/B, and SAC1.
results demonstrate that Sac1 expression in either the ER or Golgi apparatus has a minimal impact on the PI-4P that regulates OSBP activity or recruitment to contact sites
Title: Oxysterol-binding protein recruitment and activity at the endoplasmic reticulum-Golgi interface are independent of Sac1.
data suggest a model in which the 14-3-3 protein mediates SAC1 traffic from the ER through direct interaction with a sorting signal and COPII
Title: Phosphoregulatory protein 14-3-3 facilitates SAC1 transport from the endoplasmic reticulum.
Sac1 executes an essential household function in mammals that involves organization of both Golgi membranes and mitotic spindles
Title: The Sac1 phosphoinositide phosphatase regulates Golgi membrane morphology and mitotic spindle organization in mammals.
the enzymatic function of hSAC1 provides a switch for accessibility of the COPI interaction motif
Title: The human phosphatidylinositol phosphatase SAC1 interacts with the coatomer I complex.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. EBI GWAS Catalog EBI GWAS CatalogPubMed
Pharmacogenomic study of side-effects for antidepressant treatment options in STAR*D. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S3383 (e-PCR)
- UniSTS:43576

SHGC-76897 (e-PCR)
- UniSTS:648

RH124044 (e-PCR)
- UniSTS:134539

SHGC-76902 (e-PCR)
- UniSTS:47812

A004I38 (e-PCR)
- UniSTS:33779

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables phosphatase activity	ISS Inferred from Sequence or Structural Similarity more info
enables phosphatidylinositol phosphate 4-phosphatase activity	TAS Traceable Author Statement more info
enables phosphatidylinositol-3-phosphate phosphatase activity	TAS Traceable Author Statement more info
enables phosphatidylinositol-4-phosphate phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol-4-phosphate phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol-4-phosphate phosphatase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in phosphatidylinositol biosynthetic process	TAS Traceable Author Statement more info
involved_in phosphatidylinositol dephosphorylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in phosphatidylinositol dephosphorylation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	TAS Traceable Author Statement more info
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in endoplasmic reticulum-plasma membrane contact site	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: phosphatidylinositol-3-phosphatase SAC1

Names: SAC1 suppressor of actin mutations 1 like; phosphatidylinositide phosphatase SAC1; phosphatidylinositol-4-phosphate phosphatase; suppressor of actin 1; suppressor of actin mutations 1-like protein

NP_001306000.1

EC 3.1.3.64

NP_001306001.1

EC 3.1.3.64

NP_001306002.1

EC 3.1.3.64

NP_054735.3

EC 3.1.3.64

XP_011531802.1

EC 3.1.3.64

XP_054201694.1

EC 3.1.3.64

XP_054201695.1

EC 3.1.3.64

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001319071.2 → NP_001306000.1 phosphatidylinositol-3-phosphatase SAC1 isoform 1x

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the predominant transcript and encodes two isoforms, which result from the use of alternative in-frame translation termination codons. The shorter isoform (1) results from translation termination at the upstream UGA stop codon, while the longer isoform (1x) results from UGA stop codon readthrough to the downstream UGA termination codon. This RefSeq represents the longer isoform (1x). As the UGA stop codon has been reported to specify several alternative amino acids (tryptophan, cysteine, arginine and serine), its location in the longer isoform is denoted by an 'X'.

Source sequence(s)

AB020658, CA335989, DC322649

Consensus CDS

CCDS93257.1

UniProtKB/TrEMBL

A0A5F9ZHN7, A0A9L9PXW9

Related

ENSP00000500542.2, ENST00000672858.2

Conserved Domains (1) summary

COG5329
Location:57 → 513

COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
NM_001319072.2 → NP_001306001.1 phosphatidylinositol-3-phosphatase SAC1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon in the 5' region, which results in translation initiation from an alternate downstream start codon compared to variant 1. The encoded isoform (2) is shorter, with a distinct N-terminus compared to isoform 1.

Source sequence(s)

AB020658, AK296421, CA335989, DC322649

UniProtKB/TrEMBL

B4DVV3

Conserved Domains (1) summary

COG5329
Location:61 → 452

COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
NM_001319073.2 → NP_001306002.1 phosphatidylinositol-3-phosphatase SAC1 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an additional exon in the 5' region, which results in translation initiation from an in-frame, downstream start codon compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AB020658, AK301248, CA335989, DC322649

Consensus CDS

CCDS82762.1

UniProtKB/TrEMBL

B4DVV3, E9PGZ4

Related

ENSP00000396387.1, ENST00000418611.5

Conserved Domains (1) summary

COG5329
Location:19 → 410

COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]
NM_014016.5 → NP_054735.3 phosphatidylinositol-3-phosphatase SAC1 isoform 1

See identical proteins and their annotated locations for NP_054735.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the predominant transcript and encodes two isoforms, which result from the use of alternative in-frame translation termination codons. The shorter isoform (1) results from translation termination at the upstream UGA stop codon, while the longer isoform (1x) results from UGA stop codon readthrough to the downstream UGA termination codon. This RefSeq represents the shorter isoform (1).

Source sequence(s)

AB020658, CA335989, DC322649

Consensus CDS

CCDS33745.1

UniProtKB/Swiss-Prot

A8K527, B4DK71, O94935, Q7LA14, Q7LA22, Q96AX7, Q9NQ46, Q9NQ57, Q9NTJ5

UniProtKB/TrEMBL

A0A9L9PXW9

Related

ENSP00000373713.4, ENST00000389061.10

Conserved Domains (2) summary

COG5329
Location:57 → 513

COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]

pfam02383
Location:58 → 345

Syja_N; SacI homology domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

45689396..45745409

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011533500.3 → XP_011531802.1 phosphatidylinositol-3-phosphatase SAC1 isoform X1

See identical proteins and their annotated locations for XP_011531802.1

UniProtKB/TrEMBL

B4DVV3

Related

ENSP00000411966.2, ENST00000438671.4

Conserved Domains (1) summary

COG5329
Location:61 → 452

COG5329; Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]

RNA

XR_007095650.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

45705375..45761083

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054345719.1 → XP_054201694.1 phosphatidylinositol-3-phosphatase SAC1 isoform X1

UniProtKB/TrEMBL

B4DVV3
XM_054345720.1 → XP_054201695.1 phosphatidylinositol-3-phosphatase SAC1 isoform X2

UniProtKB/TrEMBL

A0A9L9PXJ6, A0A9L9PXW5