SMTNL2

smoothelin like 2

Basic information

Region (hg38): 17:4583999-4608319

Links

ENSG00000188176 ∙ NCBI:342527 ∙ ∙ HGNC:24764 ∙ Uniprot:Q2TAL5 ∙ 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 SMTNL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMTNL2 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			52	3		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	3	0

Variants in SMTNL2

This is a list of pathogenic ClinVar variants found in the SMTNL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4584616-C-T		not specified	Uncertain significance (Oct 24, 2023)
17-4584624-G-T		not specified	Uncertain significance (Nov 22, 2023)
17-4584628-A-G		not specified	Uncertain significance (Feb 26, 2024)
17-4584630-G-A		not specified	Uncertain significance (Mar 08, 2025)
17-4584633-G-C		not specified	Uncertain significance (Mar 08, 2025)
17-4584646-G-C		not specified	Uncertain significance (Feb 23, 2023)
17-4584691-G-A		not specified	Uncertain significance (Jul 10, 2024)
17-4584710-G-C		not specified	Uncertain significance (Oct 06, 2021)
17-4584849-G-A		not specified	Uncertain significance (Jul 20, 2021)
17-4584865-C-T		not specified	Uncertain significance (Sep 17, 2021)
17-4584870-G-T		not specified	Uncertain significance (Feb 01, 2025)
17-4584888-G-C		not specified	Uncertain significance (Nov 12, 2024)
17-4584897-G-A		not specified	Uncertain significance (Feb 13, 2024)
17-4584913-C-T		not specified	Uncertain significance (Feb 17, 2022)
17-4584925-G-T		not specified	Uncertain significance (Apr 01, 2024)
17-4584948-C-G		not specified	Uncertain significance (Jan 17, 2025)
17-4584961-G-C		not specified	Uncertain significance (Nov 14, 2023)
17-4584996-C-T		not specified	Uncertain significance (Aug 05, 2024)
17-4592363-T-A		not specified	Uncertain significance (Nov 24, 2024)
17-4592365-T-C		not specified	Uncertain significance (Jan 10, 2025)
17-4592386-A-G		not specified	Uncertain significance (May 06, 2024)
17-4592415-T-C		not specified	Uncertain significance (Jun 12, 2023)
17-4592966-C-A			Likely benign (Dec 01, 2022)
17-4592979-C-A		not specified	Uncertain significance (Jul 27, 2024)
17-4592979-C-G		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMTNL2	protein_coding	protein_coding	ENST00000389313	8	24321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000238	0.928	125596	0	152	125748	0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.668	186	213	0.871	0.0000136	2929
Missense in Polyphen		62	80.082	0.7742		1071
Synonymous	-0.590	97	89.9	1.08	0.00000643	972
Loss of Function	1.62	8	14.7	0.544	7.12e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00203	0.00196
Ashkenazi Jewish	0.000445	0.000397
East Asian	0.000219	0.000217
Finnish	0.0000481	0.0000462
European (Non-Finnish)	0.000898	0.000844
Middle Eastern	0.000219	0.000217
South Asian	0.000302	0.000294
Other	0.000512	0.000489

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.239
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smtnl2

Gene ontology

• Biological process: actin cytoskeleton organization
• Cellular component: microtubule organizing center;filamentous actin