SESTD1

SEC14 and spectrin domain containing 1

Basic information

Region (hg38): 2:179101678-179264832

Links

ENSG00000187231 ∙ NCBI:91404 ∙ ∙ HGNC:18379 ∙ Uniprot:Q86VW0 ∙ 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 SESTD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SESTD1 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					2	2
missense			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	30	0	2

Variants in SESTD1

This is a list of pathogenic ClinVar variants found in the SESTD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-179109984-G-C		not specified	Uncertain significance (Sep 24, 2024)
2-179112717-C-T			Likely benign (Jul 31, 2018)
2-179112730-G-A		not specified	Uncertain significance (Jun 02, 2024)
2-179112764-G-A		not specified	Uncertain significance (Aug 12, 2021)
2-179112782-C-T		not specified	Uncertain significance (Dec 10, 2024)
2-179112815-C-A		not specified	Uncertain significance (May 08, 2023)
2-179112822-C-G		not specified	Uncertain significance (Jun 04, 2024)
2-179115076-T-C		not specified	Uncertain significance (May 10, 2022)
2-179115147-A-G		not specified	Uncertain significance (Aug 12, 2024)
2-179115168-G-A		not specified	Uncertain significance (Jul 27, 2022)
2-179115174-C-A		not specified	Uncertain significance (Dec 15, 2024)
2-179115183-C-T		not specified	Uncertain significance (Feb 01, 2025)
2-179115195-C-T		not specified	Uncertain significance (Oct 08, 2024)
2-179115213-A-C		not specified	Uncertain significance (Dec 22, 2023)
2-179116713-C-T			Benign (Jul 31, 2018)
2-179116715-T-C		not specified	Uncertain significance (Jun 19, 2024)
2-179116726-T-G		not specified	Uncertain significance (Jan 29, 2025)
2-179117570-T-C		not specified	Uncertain significance (Aug 29, 2022)
2-179121862-G-C			Benign (Jun 18, 2018)
2-179121866-G-C		not specified	Uncertain significance (Jan 01, 2025)
2-179121928-A-C		not specified	Uncertain significance (Jul 14, 2021)
2-179123738-A-G		not specified	Uncertain significance (Feb 06, 2023)
2-179123790-C-T		not specified	Uncertain significance (Dec 07, 2021)
2-179124459-G-C		not specified	Uncertain significance (Dec 01, 2023)
2-179124483-C-T		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SESTD1	protein_coding	protein_coding	ENST00000428443	17	163099

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00198	125729	0	12	125741	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.31	235	358	0.657	0.0000181	4549
Missense in Polyphen		45	92.041	0.48891		1266
Synonymous	0.918	117	130	0.898	0.00000672	1252
Loss of Function	5.36	6	44.6	0.134	0.00000227	518

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000615
Ashkenazi Jewish	0.000139	0.0000992
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000534	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000660	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as the primary docking protein directing membrane turnover and assembly of the transient receptor potential channels TRPC4 and TRPC5. Binds phospholipids such as phosphatidylinositol monophosphates, phosphatidylinositol diphosphates (PIP2s) and phosphatidic acid, but not less polar lipids including phosphatidylcholine, phosphatidylserine, and phosphatidylinositol. The binding to PIP2s is calcium dependent. Might be involved in the plasma membrane localization of CTNNB1. {ECO:0000269|PubMed:20164195}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.478
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.43

Haploinsufficiency Scores

• pHI: 0.290
• hipred: Y
• hipred_score: 0.625
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.316

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sestd1
• Phenotype: renal/urinary system phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; embryo phenotype

Zebrafish Information Network

• Gene name: sestd1
• Affected structure: dorsal aorta
• Phenotype tag: abnormal
• Phenotype quality: fused with

Gene ontology

• Biological process: negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel
• Cellular component: calcium channel complex;intermediate filament cytoskeleton
• Molecular function: phosphatidylserine binding;protein binding;1-phosphatidylinositol binding;phosphatidylinositol-4,5-bisphosphate binding;phosphatidylinositol-5-phosphate binding;phosphatidylcholine binding;phosphatidylinositol-3-phosphate binding;phosphatidylinositol-3,4-bisphosphate binding;phosphatidylinositol-4-phosphate binding;phosphatidic acid binding;phosphatidylinositol-3,5-bisphosphate binding