SEC14L4

protein-coding

SEC14 like lipid binding 4, 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. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2009]

MANE transcript

NM_174977.4

Inheritance

—

ClinVar variants

U:69B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr22:30,488,902-30,505,711

External References & Databases

Ensembl (ENSG00000133488)

Transcript & Mutation Effects

hg38 • Region Span ~16.8 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 SEC14L4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 68

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174977.4. 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			1 clinvar			1
missense			66 clinvar	2 clinvar		68
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	69	2	0	71

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174977.4	RefSeq	NP_777637.1	12	MANE Select
ENST00000255858.12	Ensembl	ENSP00000255858.7	12	MANE Select
NM_001161368.3	RefSeq	NP_001154840.1	12	Standard
ENST00000320982.3	Ensembl	ENSP00000314163.3	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
lipid binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000255858
Coding exons: 12
Length: 16799
Individuals with no LoFs: 123876
Homozygous LoFs: 78
Heterozygous LoFs: 1793
Defined: 125747
p: 0.00747

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.266	229	241	0.952	0.0000140	2661
Missense (PolyPhen)		63	70.437	0.89441		903
Synonymous	-0.644	109	101	1.08	0.00000624	754
Loss of Function	1.05	20	25.8	0.776	0.00000140	255

Population LoF Frequency

Population	CAF	p-value	Status
African	0.10	0.10	notable
Latino/Admixed American	0.0048	0.0048	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00090	0.00090	rare
South Asian	0.00059	0.00059	rare
Other	0.0023	0.0023	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: 0.101

Intolerance Scores

LoFtool: 0.781
RVIS EVS: 1.07
RVIS percentile EVS: 91.67

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.211

Gene Damage Prediction

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