SEC11C

protein-coding

SEC11 homolog C, signal peptidase complex subunit

Gene summary

Enables serine-type endopeptidase activity. Involved in obsolete signal peptide processing. Located in endoplasmic reticulum membrane. Part of signal peptidase complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

SEC11L3

MANE transcript

NM_033280.4

Inheritance

—

ClinVar variants

U:8B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr18:59,139,475-59,158,832

External References & Databases

Ensembl (ENSG00000166562)

Transcript & Mutation Effects

hg38 • Region Span ~19.4 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 SEC11C variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033280.4. 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			8 clinvar	1 clinvar		9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	8	1	0	9

Loading ClinVar variants...

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_033280.4	RefSeq	NP_150596.1	6	MANE Select
ENST00000587834.6	Ensembl	ENSP00000468633.1	6	MANE Select
NM_001307941.2	RefSeq	NP_001294870.1	5	Standard
ENST00000299714.7	Ensembl	ENSP00000299714.3	4	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: ENST00000587834
Coding exons: 6
Length: 19360
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125747
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.00	49	107	0.456	0.00000560	1252
Missense (PolyPhen)		8	24.952	0.32061		291
Synonymous	0.207	38	39.7	0.958	0.00000217	363
Loss of Function	2.40	1	8.57	0.117	3.59e-7	119

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000059	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

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: 0.107

Intolerance Scores

LoFtool: 0.302
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: 0.567

Gene Damage Prediction

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