SUSD3

sushi domain containing 3, the group of Sushi domain containing

Basic information

Region (hg38): 9:93058688-93085133

Links

ENSG00000157303 ∙ NCBI:203328 ∙ OMIM:616429 ∙ HGNC:28391 ∙ Uniprot:Q96L08 ∙ 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 SUSD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUSD3 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			30	2		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	0

Variants in SUSD3

This is a list of pathogenic ClinVar variants found in the SUSD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-93058786-G-A		not specified	Uncertain significance (Nov 13, 2024)
9-93058821-A-T		not specified	Uncertain significance (Nov 27, 2023)
9-93058827-A-T		not specified	Uncertain significance (Feb 28, 2024)
9-93075802-G-A		not specified	Likely benign (Jan 26, 2025)
9-93075811-C-T		not specified	Uncertain significance (Jan 22, 2024)
9-93075834-C-T		not specified	Uncertain significance (May 17, 2023)
9-93075835-G-A		not specified	Uncertain significance (Aug 12, 2021)
9-93075841-A-G		not specified	Uncertain significance (Dec 22, 2023)
9-93075859-C-T		not specified	Uncertain significance (Dec 31, 2024)
9-93075873-C-T		not specified	Uncertain significance (Apr 08, 2022)
9-93075939-G-A		not specified	Uncertain significance (Oct 16, 2023)
9-93077884-G-A		not specified	Uncertain significance (Jan 03, 2024)
9-93077890-G-A		not specified	Uncertain significance (Jan 18, 2025)
9-93077907-T-G		not specified	Uncertain significance (Jan 23, 2023)
9-93077980-C-G		not specified	Uncertain significance (Dec 30, 2024)
9-93077981-G-A		not specified	Uncertain significance (Feb 03, 2022)
9-93079471-G-A		not specified	Likely benign (Mar 01, 2025)
9-93079515-C-T		not specified	Uncertain significance (Oct 06, 2021)
9-93079517-G-A		not specified	Uncertain significance (Mar 27, 2023)
9-93079518-T-C		not specified	Uncertain significance (Dec 02, 2024)
9-93079526-G-A		not specified	Uncertain significance (Feb 22, 2023)
9-93079535-G-C		not specified	Uncertain significance (Jul 14, 2021)
9-93079551-A-G		not specified	Uncertain significance (Jan 17, 2024)
9-93079559-G-A		not specified	Uncertain significance (Jan 24, 2023)
9-93084556-A-T		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUSD3	protein_coding	protein_coding	ENST00000375472	5	26432

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000609	0.740	125607	0	135	125742	0.000537

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	108	144	0.749	0.00000893	1639
Missense in Polyphen		37	50.437	0.73359		555
Synonymous	-0.0781	62	61.2	1.01	0.00000408	543
Loss of Function	0.932	6	9.02	0.665	5.77e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000213
Ashkenazi Jewish	0.00998	0.00837
East Asian	0.000109	0.000109
Finnish	0.0000484	0.0000462
European (Non-Finnish)	0.000358	0.000334
Middle Eastern	0.000109	0.000109
South Asian	0.0000656	0.0000653
Other	0.000176	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in breast tumorigenesis by promoting estrogen-dependent cell proliferation, cell-cell interactions and migration. {ECO:0000269|PubMed:24413080}.

Intolerance Scores

• loftool: 0.697
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.46

Haploinsufficiency Scores

• pHI: 0.0673
• hipred: N
• hipred_score: 0.180
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.222

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Susd3

Gene ontology

• Cellular component: plasma membrane;integral component of membrane