SECTM1

secreted and transmembrane 1

Basic information

Region (hg38): 17:82321023-82334074

Links

ENSG00000141574 ∙ NCBI:6398 ∙ OMIM:602602 ∙ HGNC:10707 ∙ Uniprot:Q8WVN6 ∙ 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 SECTM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SECTM1 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
missense			7	3		10
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	4	0

Variants in SECTM1

This is a list of pathogenic ClinVar variants found in the SECTM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-82322172-C-T		not specified	Likely benign (Nov 30, 2022)
17-82322249-G-A		not specified	Uncertain significance (Dec 26, 2023)
17-82322294-G-C		not specified	Uncertain significance (Jun 02, 2023)
17-82322886-G-A		not specified	Uncertain significance (Nov 06, 2023)
17-82322892-G-A			Uncertain significance (Oct 16, 2019)
17-82324627-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-82324637-C-T		not specified	Uncertain significance (Jul 19, 2023)
17-82324666-C-T		not specified	Likely benign (Jan 26, 2022)
17-82324718-G-A		not specified	Likely benign (Dec 19, 2023)
17-82324744-C-T		not specified	Uncertain significance (Nov 07, 2022)
17-82324759-C-T		not specified	Likely benign (Nov 17, 2022)
17-82327203-G-A		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SECTM1	protein_coding	protein_coding	ENST00000269389	4	13051

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0576	0.874	125723	0	3	125726	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.351	139	151	0.920	0.00000924	1579
Missense in Polyphen		30	36.951	0.81188		398
Synonymous	-1.16	81	68.8	1.18	0.00000468	532
Loss of Function	1.52	3	7.51	0.400	3.23e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in thymocyte signaling. {ECO:0000269|PubMed:15742156}.

Recessive Scores

• pRec: 0.0783

Intolerance Scores

• loftool: 0.246
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.47

Haploinsufficiency Scores

• pHI: 0.0900
• hipred: N
• hipred_score: 0.145
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.891

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sectm1a

Gene ontology

• Biological process: immune response;mesoderm development;regulation of signaling receptor activity;positive regulation of I-kappaB kinase/NF-kappaB signaling
• Cellular component: extracellular space;Golgi apparatus;plasma membrane;integral component of membrane;extracellular exosome
• Molecular function: cytokine activity