SECTM1

secreted and transmembrane 1

Basic information

Region (hg38): 17:82321024-82334074

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.

• not_specified (39 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000003004.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			33	5		38
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	6	0

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