SMTN

smoothelin

Basic information

Region (hg38): 22:31064104-31104757

Links

ENSG00000183963 ∙ NCBI:6525 ∙ OMIM:602127 ∙ HGNC:11126 ∙ Uniprot:P53814 ∙ 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 SMTN gene.

• Inborn genetic diseases (59 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMTN 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				3		3
missense			51	1	3	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8	1	1	10
Total	0	0	59	5	4

Variants in SMTN

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

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

Position	Type	Phenotype	Significance	ClinVar
22-31082927-G-A		not specified	Uncertain significance (Jul 25, 2023)
22-31082955-C-T		not specified	Likely benign (May 08, 2023)
22-31082956-G-A			Benign (Sep 11, 2018)
22-31082988-C-G		not specified	Uncertain significance (Jun 23, 2021)
22-31083236-C-T		not specified	Uncertain significance (Aug 11, 2022)
22-31083255-C-A		not specified	Uncertain significance (Aug 16, 2022)
22-31083268-G-A		not specified	Uncertain significance (May 05, 2023)
22-31083286-G-C		not specified	Uncertain significance (May 01, 2022)
22-31083296-C-T		not specified	Uncertain significance (May 16, 2023)
22-31087980-G-A		not specified	Uncertain significance (Jun 26, 2023)
22-31087999-G-T		not specified	Uncertain significance (Dec 28, 2022)
22-31088016-C-T		not specified	Uncertain significance (Aug 16, 2022)
22-31088017-G-A		not specified	Uncertain significance (Sep 06, 2022)
22-31088049-G-C		not specified	Uncertain significance (Aug 12, 2021)
22-31088086-G-A		not specified	Uncertain significance (Nov 18, 2022)
22-31088108-G-C		not specified	Uncertain significance (Mar 24, 2023)
22-31088523-C-T		not specified	Uncertain significance (Mar 14, 2023)
22-31088583-G-A		not specified	Uncertain significance (Sep 22, 2023)
22-31088726-C-A		not specified	Uncertain significance (Apr 12, 2022)
22-31088904-C-T		not specified	Uncertain significance (Aug 13, 2021)
22-31088964-T-C		not specified	Uncertain significance (Feb 15, 2023)
22-31089709-G-A		not specified	Uncertain significance (Dec 19, 2023)
22-31089721-A-T			Uncertain significance (Feb 01, 2023)
22-31089795-C-A		not specified	Uncertain significance (Apr 06, 2023)
22-31089861-G-T		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMTN	protein_coding	protein_coding	ENST00000358743	20	40653

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.60e-7	1.00	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.791	558	613	0.910	0.0000416	5938
Missense in Polyphen		181	221.27	0.81801		2046
Synonymous	1.63	212	244	0.867	0.0000153	2033
Loss of Function	3.73	20	47.9	0.418	0.00000300	481

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000276	0.000272
Ashkenazi Jewish	0.000301	0.000298
East Asian	0.000232	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000228	0.000220
Middle Eastern	0.000232	0.000217
South Asian	0.000231	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Structural protein of the cytoskeleton.

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.675
• rvis_EVS: 0.43
• rvis_percentile_EVS: 77.33

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.497
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.259

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smtn
• Phenotype: immune system phenotype; digestive/alimentary phenotype; reproductive 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); normal 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); muscle phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: smooth muscle contraction;muscle organ development;actin cytoskeleton organization
• Cellular component: cytoplasm;microtubule organizing center;cytoskeleton;actin cytoskeleton;filamentous actin
• Molecular function: actin binding;structural constituent of muscle