SECTM1

protein-coding

secreted and transmembrane 1

Gene summary

This gene encodes a transmembrane and secreted protein with characteristics of a type 1a transmembrane protein. It is found in a perinuclear Golgi-like pattern and thought to be involved in hematopoietic and/or immune system processes. [provided by RefSeq, Jul 2008]

MANE transcript

NM_003004.3

Inheritance

—

ClinVar variants

U:39B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr17:82,321,024-82,334,074

External References & Databases

Ensembl (ENSG00000141574)

Transcript & Mutation Effects

hg38 • Region Span ~13.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SECTM1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003004.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			36 clinvar	6 clinvar		42
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	7	0	46

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003004.3	RefSeq	NP_002995.1	4	MANE Select
ENST00000269389.8	Ensembl	ENSP00000269389.3	4	MANE Select
ENST00000580437.5	Ensembl	ENSP00000463904.1	4	Standard
ENST00000580437.6	Ensembl	ENSP00000463904.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

immune response
mesoderm development
regulation of signaling receptor activity
positive regulation of I-kappaB kinase/NF-kappaB signaling

Molecular Function

cytokine activity

Cellular Component

extracellular space
Golgi apparatus
plasma membrane
integral component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000269389
Coding exons: 4
Length: 13051
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125726
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.351	139	151	0.920	0.00000924	1579
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.891

Gene Damage Prediction

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