SMTNL1

smoothelin like 1

Basic information

Region (hg38): 11:57537595-57550272

Links

ENSG00000214872 ∙ NCBI:219537 ∙ OMIM:613664 ∙ HGNC:32394 ∙ Uniprot:A8MU46 ∙ 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 SMTNL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMTNL1 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			32			32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	0	0

Variants in SMTNL1

This is a list of pathogenic ClinVar variants found in the SMTNL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-57542649-C-G		not specified	Uncertain significance (Oct 18, 2021)
11-57542685-G-A		not specified	Uncertain significance (Apr 13, 2023)
11-57542695-C-G		not specified	Uncertain significance (May 13, 2022)
11-57542727-G-C		not specified	Uncertain significance (Apr 15, 2024)
11-57542739-G-A		not specified	Uncertain significance (Jul 11, 2023)
11-57542794-G-C		not specified	Uncertain significance (Nov 10, 2024)
11-57542814-G-A		not specified	Uncertain significance (Apr 13, 2023)
11-57542823-G-A		not specified	Uncertain significance (Nov 12, 2024)
11-57542844-G-A		not specified	Uncertain significance (Jul 13, 2022)
11-57542848-A-G		not specified	Uncertain significance (Sep 04, 2024)
11-57542862-G-C		not specified	Uncertain significance (Nov 04, 2023)
11-57542977-C-A		not specified	Uncertain significance (Oct 27, 2022)
11-57542995-C-T		not specified	Uncertain significance (Nov 27, 2023)
11-57543047-G-C		not specified	Uncertain significance (Dec 01, 2022)
11-57543072-G-C		not specified	Uncertain significance (Jun 25, 2024)
11-57543100-A-G		not specified	Uncertain significance (Aug 20, 2024)
11-57543108-G-A		not specified	Uncertain significance (May 20, 2024)
11-57543153-G-A		not specified	Uncertain significance (Jun 10, 2024)
11-57543173-G-T		not specified	Uncertain significance (Aug 27, 2024)
11-57543205-A-G		not specified	Uncertain significance (May 02, 2024)
11-57543367-A-G		not specified	Uncertain significance (Aug 13, 2021)
11-57543660-G-A		not specified	Uncertain significance (Aug 19, 2023)
11-57543660-G-C		not specified	Uncertain significance (Sep 09, 2024)
11-57543673-C-T		not specified	Uncertain significance (Jun 21, 2023)
11-57543720-G-C		not specified	Uncertain significance (Feb 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMTNL1	protein_coding	protein_coding	ENST00000457912	8	9130

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.67e-12	0.0744	125141	0	506	125647	0.00202

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.426	271	291	0.930	0.0000161	3312
Missense in Polyphen		72	86.472	0.83264		945
Synonymous	-1.21	132	115	1.14	0.00000705	983
Loss of Function	0.408	19	21.0	0.904	9.67e-7	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0183	0.0167
Ashkenazi Jewish	0.00	0.00
East Asian	0.000725	0.000653
Finnish	0.000102	0.0000924
European (Non-Finnish)	0.000637	0.000616
Middle Eastern	0.000725	0.000653
South Asian	0.000619	0.000555
Other	0.00139	0.00131

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of contractile properties of both striated and smooth muscles. When unphosphorylated, may inhibit myosin dephosphorylation. Phosphorylation at Ser-299 reduces this inhibitory activity (By similarity). {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.0912
• hipred: N
• hipred_score: 0.146
• ghis: 0.518

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.238

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smtnl1
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype; muscle phenotype

Gene ontology

• Biological process: actin cytoskeleton organization;positive regulation of vasoconstriction;negative regulation of blood vessel diameter
• Cellular component: nucleus;cytoplasm;microtubule organizing center;M band;I band;filamentous actin;contractile fiber
• Molecular function: calmodulin binding;tropomyosin binding;protein phosphatase 1 binding