SEC14L1

protein-coding

SEC14 like lipid binding 1, the group of SEC14 family|PRELI domain containing

Gene summary

The protein encoded by this gene belongs to the SEC14 cytosolic factor family. It has similarity to yeast SEC14 and to Japanese flying squid RALBP which suggests a possible role of the gene product in an intracellular transport system. Multiple alternatively spliced transcript variants have been found for this gene; some variants represent read-through transcripts that include exons from the upstream gene C17orf86. [provided by RefSeq, Feb 2011]

Previous symbols:

SEC14L

MANE transcript

NM_001143998.2

Inheritance

—

ClinVar variants

U:90B:10

Top phenotype

Monoclonal B-Cell Lymphocytosis

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr17:77,088,749-77,217,101

External References & Databases

Ensembl (ENSG00000129657)

Transcript & Mutation Effects

hg38 • Region Span ~128.4 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 SEC14L1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 75

not providedTotal: 11

Monoclonal B-Cell LymphocytosisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001143998.2. 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	5 clinvar	3 clinvar	9
missense			83 clinvar		2 clinvar	85
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	90	5	5	100

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001143998.2	RefSeq	NP_001137470.2	15	MANE Select
ENST00000436233.9	Ensembl	ENSP00000390392.3	15	MANE Select
NM_001039573.3	RefSeq	NP_001034662.3	16	Standard
NM_001143999.2	RefSeq	NP_001137471.2	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glucocorticoid Receptor Pathway
Nuclear Receptors Meta-Pathway

Biological Process

choline transport
negative regulation of RIG-I signaling pathway
innate immune response

Molecular Function

protein binding
RIG-I binding
molecular function regulator

Cellular Component

nucleoplasm
cytoplasm
Golgi apparatus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392476
Coding exons: 16
Length: 130382
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125748
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.43	294	437	0.672	0.0000264	4725
Missense (PolyPhen)		101	183.46	0.55051		2097
Synonymous	-0.555	187	178	1.05	0.0000119	1372
Loss of Function	4.54	8	38.3	0.209	0.00000181	444

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.000079	0.000079	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in innate immunity by inhibiting the antiviral RIG-I signaling pathway. In this pathway, functions as a negative regulator of DDX58/RIG-I, the cytoplasmic sensor of viral nucleic acids. Prevents the interaction of DDX58 with MAVS/IPS1, an important step in signal propagation (PubMed:23843640). May also regulate the SLC18A3 and SLC5A7 cholinergic transporters (PubMed:17092608). {ECO:0000269|PubMed:17092608, ECO:0000269|PubMed:23843640}.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.681
RVIS EVS: -0.62
RVIS percentile EVS: 17.4

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.367

Gene Damage Prediction

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