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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	25	0	0

Variants in SACM1L

This is a list of pathogenic ClinVar variants found in the SACM1L region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-45689476-C-T		not specified	Uncertain significance (Jan 08, 2024)
3-45689482-A-T		not specified	Uncertain significance (Jan 22, 2024)
3-45689493-A-G		not specified	Uncertain significance (Jun 02, 2024)
3-45703480-T-G		not specified	Uncertain significance (Aug 14, 2024)
3-45705141-A-C		not specified	Uncertain significance (May 20, 2024)
3-45705176-T-C		not specified	Uncertain significance (Nov 01, 2022)
3-45706791-A-G		not specified	Uncertain significance (Jan 09, 2024)
3-45706840-T-C		not specified	Uncertain significance (Dec 13, 2022)
3-45706849-C-G		not specified	Uncertain significance (Dec 22, 2023)
3-45709537-G-A		not specified	Uncertain significance (Apr 27, 2024)
3-45709543-A-C		not specified	Uncertain significance (Jun 07, 2024)
3-45709543-A-T		not specified	Uncertain significance (Jan 04, 2024)
3-45709598-G-A		not specified	Uncertain significance (Sep 06, 2022)
3-45709607-A-G		not specified	Uncertain significance (Jul 25, 2023)
3-45714053-G-A		not specified	Uncertain significance (Feb 28, 2023)
3-45719509-T-C		not specified	Uncertain significance (Jun 07, 2022)
3-45719518-G-A		not specified	Uncertain significance (Jan 30, 2024)
3-45719596-T-C		not specified	Uncertain significance (Nov 08, 2022)
3-45722015-G-C		not specified	Uncertain significance (Nov 17, 2022)
3-45722027-A-G		not specified	Uncertain significance (Sep 05, 2024)
3-45722049-T-G		not specified	Uncertain significance (Apr 10, 2023)
3-45722050-G-A		not specified	Uncertain significance (Oct 27, 2022)
3-45722903-G-A		not specified	Uncertain significance (May 08, 2024)
3-45731317-C-T		not specified	Uncertain significance (Jul 30, 2024)
3-45731325-C-G		not specified	Uncertain significance (Dec 03, 2024)

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