SACM1L

SAC1 like phosphatidylinositide phosphatase, the group of Phosphoinositide phosphatases

Basic information

Region (hg38): 3:45689056-45745412

Links

ENSG00000211456

∙ NCBI:22908 ∙ OMIM:606569 ∙ HGNC:17059 ∙ Uniprot:Q9NTJ5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SACM1L gene.

not_specified (48 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SACM1L gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014016.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			47 clinvar	1 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	47	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SACM1L	protein_coding	protein_coding	ENST00000389061	20	56369

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.695	0.305	125724	0	22	125746	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	209	307	0.680	0.0000153	3871
Missense in Polyphen		38	85.631	0.44377		1030
Synonymous	0.747	96	106	0.908	0.00000563	1042
Loss of Function	4.60	8	39.0	0.205	0.00000206	456

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000627	0.0000627
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.00	0.00
South Asian	0.0000711	0.0000653
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Phosphoinositide phosphatase that hydrolyzes phosphatidylinositol 3-phosphate (PtdIns(3)P) and phosphatidylinositol 4-phosphate (PtdIns(4)P) (PubMed:24209621). Has low activity towards PtdIns(3,5)P2 (By similarity). {ECO:0000250|UniProtKB:Q9ES21, ECO:0000269|PubMed:24209621}.;
Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Metabolism of lipids;3-phosphoinositide degradation;Metabolism;3-phosphoinositide biosynthesis;superpathway of inositol phosphate compounds;Synthesis of PIPs at the ER membrane;Synthesis of PIPs at the Golgi membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

pRec: 0.105

Intolerance Scores

loftool: 0.601
rvis_EVS: -0.42
rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

pHI: 0.555
hipred: Y
hipred_score: 0.694
ghis: 0.604

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.811

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Sacm1l
Phenotype: endocrine/exocrine gland phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype;

Gene ontology

Biological process: phosphatidylinositol biosynthetic process;phosphatidylinositol dephosphorylation
Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;integral component of endoplasmic reticulum membrane;AMPA glutamate receptor complex
Molecular function: phosphatidylinositol-3-phosphatase activity;protein binding;phosphatase activity;phosphatidylinositol bisphosphate phosphatase activity;phosphatidylinositol phosphate 4-phosphatase activity;phosphatidylinositol-4-phosphate phosphatase activity