MARCKSL1

MARCKS like 1

Basic information

Region (hg38): 1:32333839-32336233

Previous symbols: [ "MLP" ]

Links

ENSG00000175130 ∙ NCBI:65108 ∙ OMIM:602940 ∙ HGNC:7142 ∙ Uniprot:P49006 ∙ 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 MARCKSL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MARCKSL1 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				1	1	2
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	9	1	1

Variants in MARCKSL1

This is a list of pathogenic ClinVar variants found in the MARCKSL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-32334639-C-T			Benign (Aug 21, 2018)
1-32334707-C-G		not specified	Uncertain significance (Apr 29, 2024)
1-32334713-C-A		not specified	Uncertain significance (Sep 13, 2023)
1-32334719-C-T		not specified	Uncertain significance (Sep 15, 2021)
1-32334759-T-G		not specified	Uncertain significance (Nov 15, 2023)
1-32334791-C-G		not specified	Uncertain significance (Mar 16, 2022)
1-32334829-G-A		not specified	Uncertain significance (May 31, 2023)
1-32334838-G-T		not specified	Uncertain significance (Feb 02, 2022)
1-32334850-C-T		not specified	Uncertain significance (Dec 09, 2023)
1-32334851-C-T		not specified	Uncertain significance (Aug 08, 2023)
1-32334976-G-C		not specified	Uncertain significance (Jan 23, 2023)
1-32335048-C-T		not specified	Uncertain significance (Mar 31, 2024)
1-32335089-G-T			Likely benign (Jun 29, 2018)
1-32335105-G-A			Benign (Jul 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MARCKSL1	protein_coding	protein_coding	ENST00000329421	2	2548

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0143	0.695	125692	0	5	125697	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.186	107	102	1.05	0.00000489	1252
Missense in Polyphen		26	22.339	1.1639		253
Synonymous	-0.733	48	42.0	1.14	0.00000220	400
Loss of Function	0.614	3	4.39	0.684	1.83e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000367	0.0000367
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Controls cell movement by regulating actin cytoskeleton homeostasis and filopodium and lamellipodium formation (PubMed:22751924). When unphosphorylated, induces cell migration (By similarity). When phosphorylated by MAPK8, induces actin bundles formation and stabilization, thereby reducing actin plasticity, hence restricting cell movement, including neuronal migration (By similarity). May be involved in coupling the protein kinase C and calmodulin signal transduction systems (By similarity). {ECO:0000250|UniProtKB:P28667, ECO:0000269|PubMed:22751924}.
• Pathway: Fc gamma R-mediated phagocytosis - Homo sapiens (human);Leishmaniasis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.178

Intolerance Scores

• loftool: 0.409
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.614
• hipred: N
• hipred_score: 0.386
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Marcksl1
• Phenotype: reproductive system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype; embryo phenotype; hematopoietic system 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)

Zebrafish Information Network

• Gene name: marcksl1b
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: aplastic/hypoplastic

Gene ontology

• Biological process: positive regulation of cell population proliferation
• Cellular component: cytoplasm;cytoskeleton;plasma membrane;extracellular exosome
• Molecular function: actin binding;protein binding;calmodulin binding