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GeneBe

SCAND1

SCAN domain containing 1, the group of SCAN domain containing

Basic information

Region (hg38): 20:35953616-35959472

Links

ENSG00000171222NCBI:51282OMIM:610416HGNC:10566Uniprot:P57086AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCAND1 gene.

  • Inborn genetic diseases (13 variants)

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
10
clinvar
1
clinvar
11
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
?
0
non coding
?
2
clinvar
2
Total 0 0 12 1 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 Inborn genetic diseases Uncertain significance (Jun 18, 2021)2358730
20-35953865-G-C Inborn genetic diseases Uncertain significance (Nov 21, 2022)2328720
20-35953894-C-T Inborn genetic diseases Uncertain significance (Jul 12, 2022)2228434
20-35953968-G-A Inborn genetic diseases Uncertain significance (Sep 07, 2022)2311344
20-35954046-G-A Inborn genetic diseases Uncertain significance (Jun 11, 2021)2240181
20-35954061-G-A Inborn genetic diseases Uncertain significance (Mar 27, 2023)2516260
20-35954062-G-A Inborn genetic diseases Uncertain significance (Mar 29, 2023)2519983
20-35954089-C-G Inborn genetic diseases Uncertain significance (Apr 06, 2022)2281343
20-35954101-G-T Inborn genetic diseases Uncertain significance (Aug 02, 2023)2615332
20-35954113-G-C Inborn genetic diseases Uncertain significance (Aug 17, 2022)2308189
20-35954196-G-C Inborn genetic diseases Likely benign (Oct 06, 2021)2254041
20-35954536-T-C Inborn genetic diseases Uncertain significance (Mar 03, 2022)2278039
20-35954562-C-T Inborn genetic diseases Uncertain significance (Dec 19, 2022)2341542

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCAND1protein_codingprotein_codingENST00000373991 15856
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.2220.657121986011219870.00000410
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.06209293.70.9820.000004331071
Missense in Polyphen2231.2930.70303404
Synonymous-0.2984643.51.060.00000211429
Loss of Function1.0913.060.3271.34e-737

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002910.0000291
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerMediumLowMedium

Mouse Genome Informatics

Gene name
Scand1
Phenotype

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