SEC14L3

protein-coding

SEC14 like lipid binding 3, the group of SEC14 family

Gene summary

The protein encoded by this gene is highly similar to the protein encoded by the Saccharomyces cerevisiae SEC14 gene. The SEC14 protein is a phophatidylinositol transfer protein that is essential for biogenesis of Golgi-derived transport vesicles, and thus is required for the export of yeast secretory proteins from the Golgi complex. The specific function of this protein has not yet been determined. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

MANE transcript

NM_174975.5

Inheritance

—

ClinVar variants

U:69B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.22

Max pathogenic AF

—

Genomic locus

chr22:30,447,959-30,472,017

External References & Databases

Ensembl (ENSG00000100012)

Transcript & Mutation Effects

hg38 • Region Span ~24.1 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 SEC14L3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174975.5. 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			69 clinvar			69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	69	1	0	70

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174975.5	RefSeq	NP_777635.1	12	MANE Select
ENST00000215812.9	Ensembl	ENSP00000215812.5	12	MANE Select
NM_001257378.2	RefSeq	NP_001244307.1	9	Standard
NM_001257379.2	RefSeq	NP_001244308.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

lipid binding

Cellular Component

extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000215812
Coding exons: 12
Length: 24091
Individuals with no LoFs: 125257
Homozygous LoFs: 1
Heterozygous LoFs: 490
Defined: 125748
p: 0.00195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.263	231	243	0.952	0.0000141	2623
Missense (PolyPhen)		71	74.734	0.95004		854
Synonymous	0.814	85	95.1	0.894	0.00000589	740
Loss of Function	-1.04	31	25.3	1.22	0.00000130	280

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0017	0.0017	notable
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0017	0.0017	notable
Finnish	0.010	0.010	notable
European (Non-Finnish)	0.0012	0.0012	notable
South Asian	0.0016	0.0016	notable
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable hydrophobic ligand-binding protein; may play a role in the transport of hydrophobic ligands like tocopherol, squalene and phospholipids.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.762
RVIS EVS: 1.16
RVIS percentile EVS: 92.59

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.116

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High