SCAND1

SCAN domain containing 1, the group of SCAN domain containing

Basic information

Region (hg38): 20:35953616-35959472

Links

ENSG00000171222 ∙ NCBI:51282 ∙ OMIM:610416 ∙ HGNC:10566 ∙ Uniprot:P57086 ∙ 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 SCAND1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAND1 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	20	2	0

Variants in SCAND1

This is a list of pathogenic ClinVar variants found in the SCAND1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-35953800-T-G		not specified	Uncertain significance (Jun 18, 2021)
20-35953838-C-G		not specified	Uncertain significance (Nov 09, 2023)
20-35953865-G-C		not specified	Uncertain significance (Nov 21, 2022)
20-35953894-C-T		not specified	Uncertain significance (Jul 12, 2022)
20-35953968-G-A		not specified	Uncertain significance (Sep 07, 2022)
20-35953998-C-T		not specified	Uncertain significance (Sep 15, 2021)
20-35954010-C-T		not specified	Uncertain significance (Oct 10, 2023)
20-35954044-C-G		not specified	Likely benign (Dec 19, 2023)
20-35954046-G-A		not specified	Uncertain significance (Jun 11, 2021)
20-35954061-G-A		not specified	Uncertain significance (Mar 27, 2023)
20-35954062-G-A		not specified	Uncertain significance (Mar 29, 2023)
20-35954089-C-G		not specified	Uncertain significance (Apr 06, 2022)
20-35954101-G-T		not specified	Uncertain significance (Aug 02, 2023)
20-35954106-G-T		not specified	Uncertain significance (Oct 10, 2023)
20-35954113-G-C		not specified	Uncertain significance (Aug 17, 2022)
20-35954175-C-T		not specified	Uncertain significance (Jan 08, 2024)
20-35954196-G-C		not specified	Likely benign (Oct 06, 2021)
20-35954241-G-A		not specified	Uncertain significance (Oct 10, 2023)
20-35954470-G-A		not specified	Uncertain significance (May 18, 2022)
20-35954470-G-C		not specified	Uncertain significance (Sep 22, 2023)
20-35954536-T-C		not specified	Uncertain significance (Mar 03, 2022)
20-35954562-C-T		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAND1	protein_coding	protein_coding	ENST00000373991	1	5856

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.222	0.657	121986	0	1	121987	0.00000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0620	92	93.7	0.982	0.00000433	1071
Missense in Polyphen		22	31.293	0.70303		404
Synonymous	-0.298	46	43.5	1.06	0.00000211	429
Loss of Function	1.09	1	3.06	0.327	1.34e-7	37

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
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

• Function: FUNCTION: May regulate transcriptional activity.

Recessive Scores

• pRec: 0.104

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.204
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scand1

Gene ontology

• Biological process: regulation of transcription, DNA-templated;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus
• Molecular function: DNA binding;DNA-binding transcription factor activity;transcription coactivator activity;protein binding;identical protein binding