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GeneBe

SECTM1

secreted and transmembrane 1

Basic information

Region (hg38): 17:82321023-82334074

Links

ENSG00000141574NCBI:6398OMIM:602602HGNC:10707Uniprot:Q8WVN6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SECTM1 gene.

  • Inborn genetic diseases (6 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.

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
4
clinvar
2
clinvar
6
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 5 2 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)2379525
17-82322249-G-A not specified Uncertain significance (Dec 26, 2023)3159440
17-82322294-G-C not specified Uncertain significance (Jun 02, 2023)2556105
17-82322886-G-A not specified Uncertain significance (Nov 06, 2023)3159438
17-82322892-G-A Uncertain significance (Oct 16, 2019)994327
17-82324627-C-T not specified Uncertain significance (Jan 23, 2024)3159437
17-82324637-C-T not specified Uncertain significance (Jul 19, 2023)2598777
17-82324666-C-T not specified Likely benign (Jan 26, 2022)2273536
17-82324718-G-A not specified Likely benign (Dec 19, 2023)3159436
17-82324744-C-T not specified Uncertain significance (Nov 07, 2022)2322563
17-82324759-C-T not specified Likely benign (Nov 17, 2022)3159435
17-82327203-G-A not specified Uncertain significance (Mar 07, 2023)2495121

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SECTM1protein_codingprotein_codingENST00000269389 413051
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.05760.874125723031257260.0000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3511391510.9200.000009241579
Missense in Polyphen3036.9510.81188398
Synonymous-1.168168.81.180.00000468532
Loss of Function1.5237.510.4003.23e-775

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002900.0000290
Ashkenazi Jewish0.000.00
East Asian0.00005450.0000544
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.00005450.0000544
South Asian0.00003270.0000327
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sectm1a
Phenotype

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