SEC22C

protein-coding

SEC22 homolog C, vesicle trafficking protein, the group of SNAREs

Gene summary

This gene encodes a member of the SEC22 family of vesicle trafficking proteins. The encoded protein is localized to the endoplasmic reticulum and may play a role in the early stages of ER-Golgi protein trafficking. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]

Previous symbols:

SEC22L3

MANE transcript

NM_032970.4

Inheritance

—

ClinVar variants

U:42B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr3:42,547,969-42,601,080

External References & Databases

Ensembl (ENSG00000093183)

Transcript & Mutation Effects

hg38 • Region Span ~53.1 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 SEC22C variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 35

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032970.4. 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			5 clinvar			5
missense			35 clinvar	3 clinvar		38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	42	3	0	45

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032970.4	RefSeq	NP_116752.1	6	MANE Select
ENST00000264454.8	Ensembl	ENSP00000264454.3	6	MANE Select
NM_001201572.2	RefSeq	NP_001188501.1	6	Standard
NM_001201584.2	RefSeq	NP_001188513.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Post-translational protein modification
Metabolism of proteins
Transport to the Golgi and subsequent modification

Biological Process

endoplasmic reticulum to Golgi vesicle-mediated transport
protein transport

Molecular Function

protein binding

Cellular Component

endoplasmic reticulum
endoplasmic reticulum membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264454
Coding exons: 6
Length: 53112
Individuals with no LoFs: 125645
Homozygous LoFs: 0
Heterozygous LoFs: 103
Defined: 125748
p: 0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.837	137	167	0.818	0.00000858	1987
Missense (PolyPhen)		35	55.417	0.63157		688
Synonymous	0.502	58	63.1	0.920	0.00000338	596
Loss of Function	0.902	12	15.9	0.756	9.80e-7	153

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00051	0.00049	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00021	0.00020	rare
South Asian	0.0019	0.0018	notable
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in vesicle transport between the ER and the Golgi complex. {ECO:0000269|PubMed:9501016}.;

Recessive Scores

pRec: 0.0825

Intolerance Scores

LoFtool: 0.855
RVIS EVS: -0.18
RVIS percentile EVS: 39.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.149

Gene Damage Prediction

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