SCFD2

sec1 family domain containing 2

Basic information

Region (hg38): 4:52872981-53366066

Links

ENSG00000184178 ∙ NCBI:152579 ∙ ∙ HGNC:30676 ∙ Uniprot:Q8WU76 ∙ 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 SCFD2 gene.

• Inborn genetic diseases (29 variants)
• Autism, susceptiblity to (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCFD2 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		1	28	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	28	1	0

Highest pathogenic variant AF is 0.0000394

Variants in SCFD2

This is a list of pathogenic ClinVar variants found in the SCFD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-52885848-T-C		not specified	Uncertain significance (Mar 01, 2023)
4-52885851-G-A		not specified	Uncertain significance (Aug 16, 2022)
4-52885856-G-T		not specified	Uncertain significance (Jun 29, 2023)
4-52885859-C-T		not specified	Uncertain significance (Dec 21, 2021)
4-52885860-G-A		not specified	Uncertain significance (Nov 08, 2021)
4-52907525-C-T		not specified	Likely benign (Sep 15, 2021)
4-52907542-G-A		not specified	Uncertain significance (Nov 18, 2022)
4-52907584-T-C		not specified	Uncertain significance (Jun 09, 2022)
4-53145356-G-A		not specified	Uncertain significance (Feb 16, 2023)
4-53145466-T-C		not specified	Uncertain significance (Mar 28, 2023)
4-53145542-A-T		not specified	Uncertain significance (Jun 17, 2022)
4-53145564-T-A		not specified	Uncertain significance (Oct 17, 2023)
4-53273857-T-C		not specified	Uncertain significance (May 18, 2023)
4-53273890-G-C		not specified	Uncertain significance (Sep 01, 2021)
4-53273930-G-A		not specified	Uncertain significance (Oct 25, 2022)
4-53273941-G-C		not specified	Uncertain significance (Dec 20, 2023)
4-53273948-G-A		not specified	Uncertain significance (Jun 06, 2023)
4-53273969-T-C		not specified	Uncertain significance (Jun 30, 2023)
4-53273986-C-T		not specified	Uncertain significance (Oct 17, 2023)
4-53273989-G-A		Autism, susceptiblity to	Likely pathogenic (Jul 01, 2022)
4-53313674-G-A		not specified	Uncertain significance (May 23, 2023)
4-53313735-C-T		not specified	Uncertain significance (Feb 12, 2024)
4-53352622-G-A		not specified	Uncertain significance (Mar 29, 2023)
4-53352644-C-T		not specified	Uncertain significance (Sep 29, 2022)
4-53352655-A-C		not specified	Uncertain significance (Aug 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCFD2	protein_coding	protein_coding	ENST00000401642	9	493094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.02e-13	0.113	125649	1	98	125748	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.216	364	376	0.969	0.0000179	4418
Missense in Polyphen		129	129.24	0.99815		1636
Synonymous	-0.159	157	154	1.02	0.00000759	1441
Loss of Function	0.697	21	24.7	0.849	0.00000105	314

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000966	0.000963
Ashkenazi Jewish	0.000312	0.000298
East Asian	0.000716	0.000707
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000327	0.000325
Middle Eastern	0.000716	0.000707
South Asian	0.000523	0.000490
Other	0.00134	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in protein transport.

Intolerance Scores

• loftool: 0.794
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.51

Haploinsufficiency Scores

• pHI: 0.0691
• hipred: N
• hipred_score: 0.229
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.248

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scfd2

Gene ontology

• Biological process: vesicle docking involved in exocytosis;biological_process;protein transport
• Cellular component: cellular_component
• Molecular function: molecular_function