SCFD1

sec1 family domain containing 1

Basic information

Region (hg38): 14:30622290-30737694

Previous symbols: [ "C14orf163" ]

Links

ENSG00000092108 ∙ NCBI:23256 ∙ OMIM:618207 ∙ HGNC:20726 ∙ Uniprot:Q8WVM8 ∙ 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 SCFD1 gene.

• Inborn genetic diseases (19 variants)
• Amyotrophic lateral sclerosis (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCFD1 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			21			21
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	21	0	0

Variants in SCFD1

This is a list of pathogenic ClinVar variants found in the SCFD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-30630553-T-C		Amyotrophic lateral sclerosis • SCFD1-related disorder	Conflicting classifications of pathogenicity (Apr 21, 2022)
14-30633984-C-T		not specified	Uncertain significance (Mar 06, 2023)
14-30638167-A-G		not specified	Uncertain significance (Aug 17, 2022)
14-30638176-A-G		not specified	Uncertain significance (Mar 23, 2023)
14-30643390-T-C		not specified	Uncertain significance (Jan 21, 2022)
14-30649539-A-G		not specified	Uncertain significance (Jan 10, 2022)
14-30649572-A-G		not specified	Uncertain significance (Sep 29, 2023)
14-30650628-A-G		not specified	Uncertain significance (Aug 04, 2023)
14-30650657-C-T			Benign (Mar 30, 2018)
14-30653560-C-T		not specified	Uncertain significance (Dec 13, 2022)
14-30670317-G-A		not specified	Uncertain significance (Aug 11, 2022)
14-30673934-G-A		not specified	Uncertain significance (Nov 14, 2023)
14-30694794-T-G		not specified	Uncertain significance (Apr 07, 2023)
14-30694827-A-G		Amyotrophic lateral sclerosis	Conflicting classifications of pathogenicity (Jan 01, 2024)
14-30700224-T-C		not specified	Uncertain significance (Dec 15, 2023)
14-30702330-A-G		not specified	Uncertain significance (Jul 25, 2023)
14-30702341-A-C		not specified	Uncertain significance (Sep 01, 2021)
14-30705824-G-A		not specified	Uncertain significance (Jan 07, 2022)
14-30705839-G-A		not specified	Uncertain significance (Jan 18, 2022)
14-30705843-C-T		not specified	Uncertain significance (Aug 11, 2022)
14-30721906-C-T		not specified	Uncertain significance (Aug 21, 2023)
14-30722552-A-G		not specified	Uncertain significance (Jul 27, 2022)
14-30734800-G-A		not specified	Uncertain significance (Jun 14, 2023)
14-30734808-A-C		not specified	Uncertain significance (May 04, 2023)
14-30734856-C-G		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCFD1	protein_coding	protein_coding	ENST00000458591	25	113701

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000382	125722	0	10	125732	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	225	330	0.682	0.0000155	4207
Missense in Polyphen		61	107.11	0.56951		1425
Synonymous	-0.149	110	108	1.02	0.00000526	1152
Loss of Function	5.50	5	44.6	0.112	0.00000231	551

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000742	0.0000742
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.0000537	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in SNARE-pin assembly and Golgi-to-ER retrograde transport via its interaction with COG4. Involved in vesicular transport between the endoplasmic reticulum and the Golgi (By similarity). {ECO:0000250}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.511
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.227
• hipred: N
• hipred_score: 0.488
• ghis: 0.655

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scfd1

Zebrafish Information Network

• Gene name: scfd1
• Affected structure: goblet cell
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: cell morphogenesis;response to hypoxia;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;post-Golgi vesicle-mediated transport;vesicle docking involved in exocytosis;response to toxic substance;protein transport;COPII vesicle coating;regulation of protein transport;regulation of ER to Golgi vesicle-mediated transport;toxin transport;negative regulation of autophagosome assembly
• Cellular component: endoplasmic reticulum membrane;Golgi-associated vesicle;cis-Golgi network;cytosol;plasma membrane;Golgi cisterna membrane
• Molecular function: protein binding;syntaxin binding;protein-containing complex binding;protein N-terminus binding