SEC22A

protein-coding

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

Gene summary

The protein encoded by this gene belongs to the member of the SEC22 family of vesicle trafficking proteins. This protein has similarity to rat SEC22 and may act in the early stages of the secretory pathway. [provided by RefSeq, Nov 2008]

Previous symbols:

SEC22L2

MANE transcript

NM_012430.5

Inheritance

—

ClinVar variants

U:38B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr3:123,201,927-123,274,136

External References & Databases

Ensembl (ENSG00000121542)

Transcript & Mutation Effects

hg38 • Region Span ~72.2 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 SEC22A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 36

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012430.5. 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				1 clinvar		1
missense			36 clinvar	1 clinvar		37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	38	2	0	40

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012430.5	RefSeq	NP_036562.2	6	MANE Select
ENST00000492595.6	Ensembl	ENSP00000417972.1	6	MANE Select
ENST00000309934.4	Ensembl	ENSP00000310521.4	6	Standard
ENST00000309934.5	Ensembl	ENSP00000310521.4	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics
Vesicle-mediated transport
Membrane Trafficking
Post-translational protein modification
Metabolism of proteins

Biological Process

endoplasmic reticulum to Golgi vesicle-mediated transport
protein transport

Molecular Function

transporter activity
protein binding

Cellular Component

endoplasmic reticulum membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000309934
Coding exons: 6
Length: 72204
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 55
Defined: 125746
p: 0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0768	161	164	0.983	0.00000812	2004
Missense (PolyPhen)		37	44.53	0.83089		506
Synonymous	0.523	55	60.2	0.914	0.00000305	596
Loss of Function	1.01	11	15.2	0.722	8.75e-7	175

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00047	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.0011	0.0011	notable
European (Non-Finnish)	0.000079	0.000079	rare
South Asian	0.000068	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in vesicle transport between the ER and the Golgi complex. {ECO:0000250|UniProtKB:Q642F4}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.737
RVIS EVS: -0.16
RVIS percentile EVS: 41.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.786

Gene Damage Prediction

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