SUSD1

sushi domain containing 1, the group of Sushi domain containing

Basic information

Region (hg38): 9:112040783-112175297

Links

ENSG00000106868NCBI:64420HGNC:25413Uniprot:Q6UWL2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SUSD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUSD1 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
3
clinvar
3
clinvar
6
missense
36
clinvar
6
clinvar
2
clinvar
44
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 36 10 5

Variants in SUSD1

This is a list of pathogenic ClinVar variants found in the SUSD1 region.

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

Position Type Phenotype Significance ClinVar
9-112041871-C-T not specified Uncertain significance (Oct 06, 2023)3172241
9-112041882-G-C not specified Uncertain significance (Nov 09, 2024)3451455
9-112041886-G-A not specified Uncertain significance (Sep 29, 2023)3172240
9-112041911-C-T Likely benign (Dec 31, 2019)709180
9-112041931-C-T not specified Uncertain significance (Dec 05, 2022)2346651
9-112052407-T-G not specified Uncertain significance (Sep 27, 2021)2409163
9-112058445-T-C not specified Uncertain significance (Nov 18, 2022)2342535
9-112058497-A-G Likely benign (May 30, 2018)744585
9-112058601-C-T not specified Likely benign (Dec 28, 2023)3172239
9-112058622-C-A not specified Uncertain significance (Sep 26, 2024)2223303
9-112058639-G-T not specified Uncertain significance (Oct 17, 2023)3172238
9-112062979-C-T not specified Uncertain significance (Sep 25, 2024)3451453
9-112062985-A-G not specified Uncertain significance (Aug 15, 2024)3451448
9-112063019-C-T Likely benign (Jan 01, 2024)770751
9-112078557-G-A Likely benign (Jun 26, 2018)755929
9-112078586-G-C not specified Uncertain significance (Jun 10, 2022)2295333
9-112078618-G-A not specified Uncertain significance (May 31, 2023)2558268
9-112078622-G-A not specified Uncertain significance (Mar 28, 2022)2388170
9-112078658-T-C not specified Uncertain significance (Dec 20, 2021)2268084
9-112080094-C-G not specified Uncertain significance (Apr 19, 2024)3323677
9-112080173-G-A Benign (Dec 20, 2018)716152
9-112098509-G-A not specified Uncertain significance (Nov 22, 2022)2343795
9-112098524-G-C not specified Uncertain significance (Dec 13, 2022)2334550
9-112098537-C-A Likely benign (Dec 31, 2019)726097
9-112098553-G-A not specified Uncertain significance (Aug 07, 2024)3451449

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SUSD1protein_codingprotein_codingENST00000374270 16134624
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.17e-130.83112559911471257470.000589
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.033494080.8560.00002204841
Missense in Polyphen108128.830.838341559
Synonymous-0.1671591561.020.000009101484
Loss of Function1.892638.70.6710.00000197482

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001210.00120
Ashkenazi Jewish0.000.00
East Asian0.0002720.000272
Finnish0.000.00
European (Non-Finnish)0.0005900.000589
Middle Eastern0.0002720.000272
South Asian0.001470.00137
Other0.0003270.000326

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.0828

Intolerance Scores

loftool
0.485
rvis_EVS
-0.42
rvis_percentile_EVS
25.79

Haploinsufficiency Scores

pHI
0.0829
hipred
N
hipred_score
0.145
ghis
0.507

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.230

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Susd1
Phenotype

Gene ontology

Biological process
Cellular component
integral component of membrane
Molecular function
calcium ion binding