SEC14L2

SEC14 like lipid binding 2, the group of SEC14 family

Basic information

Region (hg38): 22:30396940-30425303

Previous symbols: [ "C22orf6" ]

Links

ENSG00000100003 ∙ NCBI:23541 ∙ OMIM:607558 ∙ HGNC:10699 ∙ Uniprot:O76054 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEC14L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC14L2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			13		1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	13	1	1

Variants in SEC14L2

This is a list of pathogenic ClinVar variants found in the SEC14L2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-30397150-C-G		not specified	Uncertain significance (Dec 28, 2023)
22-30399716-G-A		not specified	Uncertain significance (Apr 17, 2023)
22-30406381-G-A		not specified	Uncertain significance (Dec 21, 2023)
22-30407108-G-A		not specified	Uncertain significance (Dec 17, 2023)
22-30407128-A-G		not specified	Uncertain significance (Jan 09, 2024)
22-30407568-C-A		not specified	Uncertain significance (Jan 02, 2024)
22-30407590-A-G			Benign (Jun 13, 2018)
22-30409214-A-G		not specified	Uncertain significance (Apr 12, 2022)
22-30409259-C-G		not specified	Uncertain significance (Dec 20, 2023)
22-30409292-A-T			Likely benign (Aug 16, 2018)
22-30409454-C-A		not specified	Uncertain significance (Aug 05, 2023)
22-30409456-G-A		not specified	Uncertain significance (Dec 01, 2022)
22-30415794-C-T		not specified	Uncertain significance (Apr 24, 2023)
22-30415803-G-A		not specified	Uncertain significance (Feb 02, 2022)
22-30415957-G-A		not specified	Uncertain significance (Sep 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC14L2	protein_coding	protein_coding	ENST00000312932	12	28460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.92e-8	0.919	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.989	187	229	0.816	0.0000123	2640
Missense in Polyphen		87	118.04	0.73706		1327
Synonymous	-0.516	94	87.8	1.07	0.00000465	756
Loss of Function	1.81	16	25.9	0.617	0.00000135	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000496	0.000496
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000326	0.000326
South Asian	0.000327	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Carrier protein. Binds to some hydrophobic molecules and promotes their transfer between the different cellular sites. Binds with high affinity to alpha-tocopherol. Also binds with a weaker affinity to other tocopherols and to tocotrienols. May have a transcriptional activatory activity via its association with alpha-tocopherol. Probably recognizes and binds some squalene structure, suggesting that it may regulate cholesterol biosynthesis by increasing the transfer of squalene to a metabolic active pool in the cell.
• Pathway: Validated transcriptional targets of deltaNp63 isoforms (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.552
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.280
• hipred: N
• hipred_score: 0.396
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.223

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sec14l2
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of cholesterol biosynthetic process;positive regulation of transcription, DNA-templated
• Cellular component: nucleus;cytoplasm;cytosol;extracellular exosome
• Molecular function: phospholipid binding;vitamin E binding