SEC14L6

Summary

SEC14L6 (SEC14 like lipid binding 6, HGNC:40047) is a protein-coding gene on chromosome 22q12.2, encoding SEC14-like protein 6 (B5MCN3).

Predicted to be active in cytoplasm.

Source: NCBI Gene 730005 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 93 total
• MANE Select transcript: NM_001193336

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40047
Approved symbol	SEC14L6
Name	SEC14 like lipid binding 6
Location	22q12.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000214491
Ensembl biotype	protein_coding
Entrez	730005

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000402034, ENST00000437871, ENST00000687231, ENST00000687338, ENST00000688644, ENST00000691669

RefSeq mRNA: 3 — MANE Select: NM_001193336 NM_001193336, NM_001353441, NM_001353443

CCDS: CCDS54518, CCDS93146, CCDS93147

Canonical transcript exons

ENST00000402034 — 12 exons

Exon	Start	End
ENSE00001548292	30522799	30525109
ENSE00001549348	30546629	30546741
ENSE00001551128	30531903	30531998
ENSE00001551260	30532525	30532713
ENSE00001552675	30529289	30529349
ENSE00001554364	30532797	30532856
ENSE00001564481	30533996	30534039
ENSE00001686228	30525350	30525519
ENSE00001704408	30538827	30538902
ENSE00001726493	30529087	30529170
ENSE00001774390	30525611	30525750
ENSE00001806781	30525826	30525932

Expression profiles

Bgee: expression breadth ubiquitous, 123 present calls, max score 83.06.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2231 / max 16.4304, expressed in 121 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193636	0.1841	105
193637	0.0390	17

Top tissues by expression

136 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
quadriceps femoris	UBERON:0001377	83.06	gold quality
metanephros cortex	UBERON:0010533	79.63	gold quality
thymus	UBERON:0002370	78.69	silver quality
adult mammalian kidney	UBERON:0000082	77.30	gold quality
islet of Langerhans	UBERON:0000006	76.67	gold quality
cerebellar vermis	UBERON:0004720	76.67	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.14	silver quality
kidney	UBERON:0002113	75.05	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	74.34	gold quality
spinal cord	UBERON:0002240	73.84	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	73.81	gold quality
cortex of kidney	UBERON:0001225	73.75	gold quality
gall bladder	UBERON:0002110	73.43	gold quality
substantia nigra	UBERON:0002038	72.75	gold quality
pancreas	UBERON:0001264	72.25	gold quality
caudate nucleus	UBERON:0001873	72.10	gold quality
hypothalamus	UBERON:0001898	71.94	gold quality
amygdala	UBERON:0001876	71.66	gold quality
upper lobe of left lung	UBERON:0008952	71.50	gold quality
temporal lobe	UBERON:0001871	71.34	gold quality
putamen	UBERON:0001874	71.17	gold quality
right lung	UBERON:0002167	71.06	gold quality
nucleus accumbens	UBERON:0001882	70.65	gold quality
body of pancreas	UBERON:0001150	70.19	gold quality
anterior cingulate cortex	UBERON:0009835	69.49	gold quality
lung	UBERON:0002048	69.43	gold quality
right testis	UBERON:0004534	68.94	gold quality
testis	UBERON:0000473	68.52	gold quality
Ammon’s horn	UBERON:0001954	68.38	gold quality
left testis	UBERON:0004533	68.14	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.69

Regulation

Is transcription factor: no

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	sec14l8	ENSDARG00000059729
danio_rerio	sec14l7	ENSDARG00000099633
drosophila_melanogaster	retm	FBGN0031814
drosophila_melanogaster	CG13893	FBGN0035146
caenorhabditis_elegans		WBGENE00007925
caenorhabditis_elegans		WBGENE00009241
caenorhabditis_elegans	ctg-1	WBGENE00010370
caenorhabditis_elegans		WBGENE00011962

Paralogs (6): SEC14L2 (ENSG00000100003), SEC14L3 (ENSG00000100012), SEC14L5 (ENSG00000103184), SEC14L1 (ENSG00000129657), SEC14L4 (ENSG00000133488), TTPA (ENSG00000137561)

Protein

Protein identifiers

SEC14-like protein 6 — B5MCN3 (reviewed: B5MCN3)

All UniProt accessions (6): A0A8I5KSJ2, A0A8I5KTV1, A0A8I5KVX3, A0A8I5QKM7, B5MCN3, H7C077

RefSeq proteins (3): NP_001180265, NP_001340370, NP_001340372 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001251	CRAL-TRIO_dom	Domain
IPR009038	GOLD_dom	Domain
IPR011074	CRAL/TRIO_N_dom	Domain
IPR036273	CRAL/TRIO_N_dom_sf	Homologous_superfamily
IPR036598	GOLD_dom_sf	Homologous_superfamily
IPR036865	CRAL-TRIO_dom_sf	Homologous_superfamily
IPR051064

Pfam: PF00650

UniProt features (3 total): domain 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-B5MCN3-F1	94.20	0.88

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 5 (showing top): NFKBIA_TARGET_GENES, ZNF37A_TARGET_GENES, chr22q12, DESCARTES_MAIN_FETAL_PAEP_MECOM_POSITIVE_CELLS, DESCARTES_FETAL_PLACENTA_PAEP_MECOM_POSITIVE_CELLS

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

390 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SEC14L6	C11orf96	Q7Z7L8	513
SEC14L6	ZNF735	P0CB33	480
SEC14L6	DCAKD	Q8WVC6	432
SEC14L6	OXCT2	Q9BYC2	419
SEC14L6	FAM117B	Q6P1L5	417
SEC14L6	SLC25A44	Q96H78	413
SEC14L6	ICA1L	Q8NDH6	399
SEC14L6	NBEAL1	Q6ZS30	397
SEC14L6	ZNF727	A8MUV8	370
SEC14L6	SHISA9	B4DS77	370
SEC14L6	TRIM47	Q96LD4	348
SEC14L6	FAM221A	A4D161	333
SEC14L6	CYS1	Q717R9	331
SEC14L6	GNG4	P50150	329
SEC14L6	ADAMTSL4	Q6UY14	324

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: B0JYW5, B0X4N1, B1AS42, B3MF31, B3MZN7, B3NY19, B4P925, B4PYH5, B5MCN3, D3ZEY4, O19114, P20192, P55205, Q16P87, Q28C60, Q28CZ9, Q2KHV5, Q2NKY8, Q32LH7, Q3MHU3, Q3TDX8, Q3TIU4, Q502I6, Q5BJS0, Q5E9L5, Q5R607, Q5ZKD7, Q653S9, Q68EJ0, Q68EZ3, Q6DCK1, Q6IPT4, Q6L8Q7, Q6NZB1, Q6P5E8, Q6Q2C2, Q6TL19, Q6ZSI9, Q7L1T6, Q7L2E3

Diamond homologs: A8Y5H7, B5MCN3, F4IHJ0, F4J7S8, F4JLE5, F4JVA6, F4JVA9, F4JYJ3, F4K6D3, O43304, O76054, P49193, P58875, Q03606, Q0V9N0, Q16KN5, Q29JQ0, Q7PWB1, Q8GXC6, Q8R0F9, Q92503, Q93ZE9, Q94A34, Q99J08, Q99MS0, Q9SI13, Q9SIW3, Q9UDX3, Q9UDX4, Q9VMD6, Q9Z1J8, Q10137, F4HP88, P24280, Q75DK1, A6ZQI5, O17907, P41034, P47008, P49638

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

93 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	82
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2366 predictions. Top by Δscore:

Variant	Effect	Δscore
22:30525605:CCCTA:C	donor_loss	1.0000
22:30525606:CCTA:C	donor_loss	1.0000
22:30525608:TA:T	donor_loss	1.0000
22:30525609:ACC:A	donor_loss	1.0000
22:30525751:C:CA	acceptor_loss	1.0000
22:30525751:C:CC	acceptor_gain	1.0000
22:30525821:TGTA:T	donor_loss	1.0000
22:30525822:GTAC:G	donor_loss	1.0000
22:30525823:TA:T	donor_loss	1.0000
22:30525825:C:CT	donor_loss	1.0000
22:30525928:GTTGT:G	acceptor_gain	1.0000
22:30525929:TTGT:T	acceptor_gain	1.0000
22:30525930:TGT:T	acceptor_gain	1.0000
22:30525931:GT:G	acceptor_gain	1.0000
22:30525933:C:CA	acceptor_loss	1.0000
22:30525933:C:CC	acceptor_gain	1.0000
22:30525934:T:A	acceptor_loss	1.0000
22:30529350:C:CC	acceptor_gain	1.0000
22:30532791:GCTCA:G	donor_loss	1.0000
22:30532792:CTCA:C	donor_loss	1.0000
22:30532793:TCA:T	donor_loss	1.0000
22:30532794:CA:C	donor_loss	1.0000
22:30532795:A:AC	donor_gain	1.0000
22:30532795:ACCTC:A	donor_loss	1.0000
22:30532796:C:CC	donor_gain	1.0000
22:30532796:CCT:C	donor_gain	1.0000
22:30532855:TG:T	acceptor_gain	1.0000
22:30532857:C:CC	acceptor_gain	1.0000
22:30533998:T:A	donor_gain	1.0000
22:30538821:CCTTA:C	donor_loss	1.0000

AlphaMissense

2618 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:30525510:A:C	F307L	0.956
22:30525510:A:T	F307L	0.956
22:30525512:A:G	F307L	0.956
22:30525483:A:C	F316L	0.945
22:30525483:A:T	F316L	0.945
22:30525485:A:G	F316L	0.945
22:30532845:G:C	F62L	0.938
22:30532845:G:T	F62L	0.938
22:30532847:A:G	F62L	0.938
22:30534029:A:C	F47L	0.935
22:30534029:A:T	F47L	0.935
22:30534031:A:G	F47L	0.935
22:30538836:A:G	W41R	0.930
22:30538836:A:T	W41R	0.930
22:30525096:A:C	F365L	0.915
22:30525096:A:T	F365L	0.915
22:30525098:A:G	F365L	0.915
22:30532655:A:T	V98D	0.914
22:30525874:A:C	F241L	0.912
22:30525874:A:T	F241L	0.912
22:30525876:A:G	F241L	0.912
22:30525518:A:G	W305R	0.910
22:30525518:A:T	W305R	0.910
22:30525474:G:C	F319L	0.902
22:30525474:G:T	F319L	0.902
22:30525476:A:G	F319L	0.902
22:30533999:C:A	R57S	0.866
22:30533999:C:G	R57S	0.866
22:30525887:A:G	L237P	0.861
22:30525511:A:G	F307S	0.860

dbSNP variants (sampled 300 via entrez): RS1000027493 (22:30545441 C>T), RS1000280726 (22:30547692 A>C,G), RS1000312466 (22:30543583 T>C), RS1000387926 (22:30541490 C>T), RS1000440377 (22:30541759 G>C), RS1000540059 (22:30537608 AGAGC>A), RS1000661687 (22:30532159 C>A,G,T), RS1000667861 (22:30529276 C>A,G,T), RS1000693588 (22:30548034 G>C), RS1001008843 (22:30534992 C>T), RS1001179090 (22:30538418 A>G), RS1001272455 (22:30538564 C>A,G), RS1001273108 (22:30523464 C>A), RS1001409 (22:30522838 A>G), RS1001434167 (22:30527128 A>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST010241_64	Apolipoprotein A1 levels	3.000000e-14
GCST010242_303	HDL cholesterol levels	2.000000e-14
GCST010703_155	Brain morphology (MOSTest)	3.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004614	apolipoprotein A 1 measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
tris(2-butoxyethyl) phosphate	affects expression	1
sodium arsenite	increases expression	1
aflatoxin B2	decreases methylation	1
Leflunomide	increases expression	1
Malathion	decreases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.