SUSD2

sushi domain containing 2, the group of Sushi domain containing

Basic information

Region (hg38): 22:24181487-24189106

Links

ENSG00000099994 ∙ NCBI:56241 ∙ OMIM:615825 ∙ HGNC:30667 ∙ Uniprot:Q9UGT4 ∙ 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 SUSD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUSD2 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				7	1	8
missense			69	7	3	79
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	69	14	4

Variants in SUSD2

This is a list of pathogenic ClinVar variants found in the SUSD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-24181530-C-A		not specified	Uncertain significance (Oct 27, 2023)
22-24181563-C-T			Benign (Jun 26, 2018)
22-24183088-C-T			Likely benign (Jan 01, 2023)
22-24183105-G-A		not specified	Uncertain significance (Oct 12, 2021)
22-24183116-C-T		not specified	Uncertain significance (Jul 14, 2022)
22-24183117-C-T		not specified	Uncertain significance (Oct 16, 2023)
22-24183156-G-C		not specified	Uncertain significance (Apr 05, 2023)
22-24183203-G-A		not specified	Uncertain significance (Mar 20, 2023)
22-24183222-G-A		not specified	Likely benign (Apr 20, 2023)
22-24183230-A-C		not specified	Uncertain significance (Nov 10, 2022)
22-24183231-A-G		not specified	Uncertain significance (Apr 19, 2023)
22-24183520-G-A		not specified	Uncertain significance (Jan 10, 2022)
22-24183580-C-T		not specified	Uncertain significance (Feb 02, 2022)
22-24183625-C-T		not specified	Uncertain significance (Oct 06, 2021)
22-24183628-G-T		not specified	Likely benign (Oct 13, 2023)
22-24183629-C-T		not specified	Uncertain significance (Oct 26, 2022)
22-24184138-C-T		not specified	Uncertain significance (May 17, 2024)
22-24184188-G-A			Benign/Likely benign (Jan 01, 2023)
22-24184204-G-A		not specified	Uncertain significance (Jun 07, 2024)
22-24184217-C-G		not specified	Uncertain significance (Dec 11, 2023)
22-24184253-C-G		not specified	Uncertain significance (Aug 28, 2023)
22-24184291-T-A		not specified	Uncertain significance (Nov 08, 2022)
22-24184802-C-T		not specified	Uncertain significance (Jul 27, 2021)
22-24184807-C-G		not specified	Uncertain significance (Sep 20, 2023)
22-24184840-G-A		not specified	Uncertain significance (Jan 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUSD2	protein_coding	protein_coding	ENST00000358321	15	7852

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-21	0.0209	125414	1	330	125745	0.00132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.111	526	533	0.986	0.0000361	5238
Missense in Polyphen		169	179.64	0.94077		1982
Synonymous	-0.673	254	241	1.06	0.0000185	1672
Loss of Function	0.980	36	42.9	0.839	0.00000239	404

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00843	0.00835
Ashkenazi Jewish	0.00	0.00
East Asian	0.00115	0.00114
Finnish	0.00	0.00
European (Non-Finnish)	0.000630	0.000615
Middle Eastern	0.00115	0.00114
South Asian	0.00138	0.00137
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a cytokine receptor for C10ORF99. May be a tumor suppressor; together with C10ORF99 has a growth inhibitory effect on colon cancer cells which includes G1 cell cycle arrest (PubMed:25351403). May play a role in breast tumorigenesis (PubMed:23131994). {ECO:0000269|PubMed:23131994, ECO:0000269|PubMed:25351403}.

Recessive Scores

• pRec: 0.0883

Intolerance Scores

• loftool: 0.890
• rvis_EVS: -1.07
• rvis_percentile_EVS: 7.35

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.267
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Susd2

Gene ontology

• Biological process: receptor-mediated endocytosis;immune response;negative regulation of cell division;negative regulation of cell cycle G1/S phase transition
• Cellular component: plasma membrane;integral component of membrane;extracellular exosome
• Molecular function: scavenger receptor activity;protein binding;polysaccharide binding