SCP2D1

SCP2 sterol binding domain containing 1

Basic information

Region (hg38): 20:18813783-18814378

Previous symbols: [ "C20orf79" ]

Links

ENSG00000132631 ∙ NCBI:140856 ∙ ∙ HGNC:16211 ∙ Uniprot:Q9UJQ7 ∙ 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 SCP2D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCP2D1 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in SCP2D1

This is a list of pathogenic ClinVar variants found in the SCP2D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-18813878-G-T		not specified	Uncertain significance (Jan 31, 2022)
20-18813891-G-A		not specified	Uncertain significance (Oct 08, 2024)
20-18813897-G-A		not specified	Uncertain significance (Aug 17, 2022)
20-18813898-T-A		not specified	Uncertain significance (Feb 12, 2024)
20-18813909-G-A		not specified	Uncertain significance (Feb 12, 2024)
20-18813944-G-T		not specified	Uncertain significance (Aug 16, 2022)
20-18813970-G-A		not specified	Uncertain significance (Nov 25, 2024)
20-18814002-G-C		not specified	Uncertain significance (Aug 27, 2024)
20-18814100-G-A		not specified	Uncertain significance (Sep 08, 2024)
20-18814105-C-T		not specified	Likely benign (Jan 03, 2022)
20-18814117-G-C		not specified	Uncertain significance (Nov 08, 2024)
20-18814122-C-A		not specified	Uncertain significance (Sep 03, 2024)
20-18814147-C-T		not specified	Uncertain significance (Feb 13, 2024)
20-18814162-T-C		not specified	Uncertain significance (Feb 05, 2024)
20-18814179-A-G		not specified	Uncertain significance (Dec 30, 2023)
20-18814237-T-C		not specified	Uncertain significance (May 28, 2024)
20-18814266-A-G		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCP2D1	protein_coding	protein_coding	ENST00000377428	1	664

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00716	0.550	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.354	76	85.2	0.892	0.00000431	1028
Missense in Polyphen		25	24.25	1.0309		324
Synonymous	0.725	28	33.3	0.840	0.00000195	306
Loss of Function	0.0896	3	3.17	0.946	1.34e-7	46

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.22

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scp2d1

Gene ontology

• Biological process: steroid biosynthetic process;phospholipid transport;positive regulation of intracellular cholesterol transport