SEC14L5

SEC14 like lipid binding 5, the group of SEC14 family|PRELI domain containing

Basic information

Region (hg38): 16:4958330-5019157

Links

ENSG00000103184 ∙ NCBI:9717 ∙ OMIM:619412 ∙ HGNC:29032 ∙ Uniprot:O43304 ∙ 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 SEC14L5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC14L5 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			53	3		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	3	0

Variants in SEC14L5

This is a list of pathogenic ClinVar variants found in the SEC14L5 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-4959352-G-A		not specified	Uncertain significance (Oct 27, 2022)
16-4959360-A-G		not specified	Uncertain significance (Jun 29, 2022)
16-4987647-G-A		not specified	Uncertain significance (Dec 11, 2023)
16-4988149-A-T		not specified	Uncertain significance (Mar 01, 2023)
16-4988156-G-C		not specified	Uncertain significance (Oct 12, 2021)
16-4988196-C-G		not specified	Uncertain significance (May 23, 2024)
16-4988197-T-A		not specified	Uncertain significance (Jan 29, 2024)
16-4988206-A-G		not specified	Uncertain significance (Dec 19, 2022)
16-4988212-C-T		not specified	Uncertain significance (Oct 13, 2023)
16-4988231-A-G		not specified	Uncertain significance (Aug 17, 2022)
16-4988252-T-C		not specified	Uncertain significance (Jan 08, 2024)
16-4990771-A-G		not specified	Uncertain significance (Aug 27, 2024)
16-4990851-T-A		not specified	Uncertain significance (Aug 11, 2024)
16-4990885-A-G		not specified	Uncertain significance (Dec 04, 2024)
16-4990890-A-G		not specified	Uncertain significance (Apr 27, 2023)
16-4991899-C-T		not specified	Uncertain significance (Aug 21, 2023)
16-4991919-G-A		not specified	Uncertain significance (Aug 30, 2021)
16-4991937-C-T		not specified	Uncertain significance (Apr 06, 2022)
16-4991953-C-T		not specified	Uncertain significance (Jan 17, 2023)
16-4991979-C-G		not specified	Uncertain significance (May 13, 2024)
16-4992016-C-T		not specified	Uncertain significance (Oct 20, 2023)
16-4992021-A-G		not specified	Likely benign (May 17, 2023)
16-4992022-G-A		not specified	Uncertain significance (Jan 29, 2024)
16-4996352-C-G		not specified	Uncertain significance (Nov 26, 2024)
16-4996363-C-G		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC14L5	protein_coding	protein_coding	ENST00000251170	15	60842

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.09e-22	0.00269	124556	2	144	124702	0.000586

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.43	507	424	1.20	0.0000271	4473
Missense in Polyphen		147	133.97	1.0973		1495
Synonymous	-3.64	238	176	1.35	0.0000113	1362
Loss of Function	0.339	34	36.2	0.939	0.00000189	387

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000838	0.000835
Ashkenazi Jewish	0.00	0.00
East Asian	0.000396	0.000389
Finnish	0.000421	0.000418
European (Non-Finnish)	0.000592	0.000584
Middle Eastern	0.000396	0.000389
South Asian	0.00145	0.00137
Other	0.000339	0.000330

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.599
• rvis_EVS: -1.7
• rvis_percentile_EVS: 2.54

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.254
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.470

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sec14l5