SEC11A

protein-coding

SEC11 homolog A, signal peptidase complex subunit

Gene summary

This gene encodes a member of the peptidase S26B family. The encoded protein is an 18kDa subunit of the signal peptidase complex and has been linked to cell migration and invasion, gastric cancer and lymph node metastasis. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 8. [provided by RefSeq, Dec 2012]

Previous symbols:

SEC11L1

MANE transcript

NM_014300.4

Inheritance

—

ClinVar variants

U:20

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr15:84,669,538-84,716,460

External References & Databases

Ensembl (ENSG00000140612)

Transcript & Mutation Effects

hg38 • Region Span ~46.9 kb

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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 SEC11A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014300.4. 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						0
missense			18 clinvar			18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	20	0	0	20

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014300.4	RefSeq	NP_055115.1	6	MANE Select
ENST00000268220.12	Ensembl	ENSP00000268220.7	6	MANE Select
NM_001271918.2	RefSeq	NP_001258847.1	5	Standard
NM_001271919.2	RefSeq	NP_001258848.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Protein export - Homo sapiens (human)
Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP)
Incretin synthesis, secretion, and inactivation
Peptide hormone metabolism
SRP-dependent cotranslational protein targeting to membrane

Biological Process

signal peptide processing

Molecular Function

peptidase activity
serine-type peptidase activity

Cellular Component

signal peptidase complex
endoplasmic reticulum membrane
integral component of membrane
organelle membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000268220
Coding exons: 6
Length: 47173
Individuals with no LoFs: 124595
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 124603
p: 0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.58	53	96.8	0.547	0.00000496	1161
Missense (PolyPhen)		15	40.266	0.37252		459
Synonymous	0.439	31	34.3	0.905	0.00000183	346
Loss of Function	1.59	6	11.9	0.504	8.41e-7	118

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000069	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0	0.0	absent
Other	0.00021	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the microsomal signal peptidase complex which removes signal peptides from nascent proteins as they are translocated into the lumen of the endoplasmic reticulum. {ECO:0000250}.;

Recessive Scores

pRec: 0.142

Intolerance Scores

LoFtool: 0.437
RVIS EVS: -0.03
RVIS percentile EVS: 51.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.781

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low