SEC14L4

SEC14 like lipid binding 4, the group of SEC14 family

Basic information

Region (hg38): 22:30488902-30505711

Links

ENSG00000133488 ∙ NCBI:284904 ∙ OMIM:612825 ∙ HGNC:20627 ∙ Uniprot:Q9UDX3 ∙ 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 SEC14L4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC14L4 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			34	2		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	2	0

Variants in SEC14L4

This is a list of pathogenic ClinVar variants found in the SEC14L4 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-30490124-G-T		not specified	Uncertain significance (Feb 15, 2025)
22-30490132-G-C		not specified	Uncertain significance (Nov 11, 2024)
22-30490163-C-T		not specified	Uncertain significance (Sep 26, 2023)
22-30490217-G-A		not specified	Uncertain significance (Aug 13, 2021)
22-30491584-T-C		not specified	Uncertain significance (Aug 15, 2023)
22-30491633-G-A		not specified	Uncertain significance (Feb 16, 2023)
22-30491667-A-C		not specified	Likely benign (Aug 23, 2021)
22-30491680-C-T		not specified	Uncertain significance (Jan 04, 2024)
22-30491856-G-C		not specified	Uncertain significance (Jul 19, 2023)
22-30491862-C-T		not specified	Uncertain significance (Jun 30, 2024)
22-30491915-T-C		not specified	Uncertain significance (Dec 14, 2024)
22-30491931-C-T		not specified	Uncertain significance (Sep 26, 2024)
22-30492098-A-G		not specified	Uncertain significance (Feb 07, 2023)
22-30492486-C-T		not specified	Uncertain significance (Jul 25, 2024)
22-30492494-C-T		not specified	Likely benign (Oct 26, 2021)
22-30492495-T-C		not specified	Uncertain significance (Oct 17, 2023)
22-30492512-A-G		not specified	Uncertain significance (Feb 09, 2025)
22-30492527-A-C		not specified	Uncertain significance (Nov 01, 2022)
22-30494179-T-C		not specified	Uncertain significance (Jun 07, 2023)
22-30494879-T-G		not specified	Uncertain significance (Jan 30, 2024)
22-30494915-C-T		not specified	Uncertain significance (Aug 05, 2024)
22-30494925-C-T		not specified	Uncertain significance (Jan 07, 2025)
22-30494946-C-T		not specified	Uncertain significance (Nov 12, 2021)
22-30495312-C-T		not specified	Uncertain significance (Dec 12, 2023)
22-30495349-C-G		not specified	Uncertain significance (Oct 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC14L4	protein_coding	protein_coding	ENST00000255858	12	16799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.31e-11	0.322	123876	78	1793	125747	0.00747

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.266	229	241	0.952	0.0000140	2661
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.106	0.106
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000901	0.000897
Middle Eastern	0.0000544	0.0000544
South Asian	0.000591	0.000588
Other	0.00230	0.00228

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.279
• hipred: N
• hipred_score: 0.259
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.211

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sec14l4

Gene ontology

• Molecular function: protein binding;lipid binding