SUSD4

sushi domain containing 4, the group of Sushi domain containing

Basic information

Region (hg38): 1:223220818-223364233

Links

ENSG00000143502 ∙ NCBI:55061 ∙ OMIM:615827 ∙ HGNC:25470 ∙ Uniprot:Q5VX71 ∙ 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 SUSD4 gene.

• Inborn genetic diseases (27 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUSD4 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			24	3		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	3	0

Variants in SUSD4

This is a list of pathogenic ClinVar variants found in the SUSD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-223223281-G-T		not specified	Uncertain significance (Apr 20, 2023)
1-223223296-G-A		not specified	Uncertain significance (Nov 17, 2022)
1-223223350-C-G		not specified	Uncertain significance (Jul 11, 2023)
1-223223375-G-A		not specified	Uncertain significance (Jun 24, 2022)
1-223223383-G-A		not specified	Uncertain significance (Sep 14, 2023)
1-223223510-T-G		not specified	Likely benign (Feb 03, 2022)
1-223223573-C-T		not specified	Uncertain significance (May 08, 2023)
1-223223609-T-C		not specified	Uncertain significance (Dec 21, 2022)
1-223223620-C-T		not specified	Uncertain significance (Jan 18, 2022)
1-223223621-G-A		not specified	Uncertain significance (Feb 21, 2024)
1-223227646-C-T		not specified	Uncertain significance (Jun 17, 2022)
1-223229220-T-A		not specified	Uncertain significance (Jul 19, 2023)
1-223229243-C-A		not specified	Uncertain significance (Oct 27, 2022)
1-223229338-G-A		not specified	Uncertain significance (May 24, 2023)
1-223229350-C-T		not specified	Likely benign (Nov 08, 2022)
1-223229359-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-223264647-C-G		not specified	Uncertain significance (Jul 27, 2022)
1-223264648-G-C		not specified	Uncertain significance (Apr 05, 2023)
1-223264738-T-C		not specified	Uncertain significance (Dec 12, 2023)
1-223264795-A-T		not specified	Likely benign (Dec 28, 2022)
1-223268540-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-223268594-T-C		not specified	Uncertain significance (Nov 02, 2023)
1-223268669-C-T		not specified	Uncertain significance (May 05, 2023)
1-223292442-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-223292573-A-G		not specified	Uncertain significance (Dec 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUSD4	protein_coding	protein_coding	ENST00000343846	8	143384

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000145	0.993	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.699	258	292	0.885	0.0000168	3185
Missense in Polyphen		89	117.43	0.75789		1268
Synonymous	0.329	122	127	0.963	0.00000861	965
Loss of Function	2.37	10	22.0	0.454	0.00000102	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000908	0.0000908
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000105
Middle Eastern	0.000220	0.000217
South Asian	0.000199	0.000196
Other	0.000346	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as complement inhibitor by disrupting the formation of the classical C3 convertase. Isoform 3 inhibits the classical complement pathway, while membrane-bound isoform 1 inhibits deposition of C3b via both the classical and alternative complement pathways. {ECO:0000269|PubMed:23482636}.

Intolerance Scores

• loftool: 0.673
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.78

Haploinsufficiency Scores

• pHI: 0.202
• hipred: N
• hipred_score: 0.342
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.100

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Susd4

Zebrafish Information Network

• Gene name: susd4
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curved

Gene ontology

• Biological process: complement activation, classical pathway;regulation of complement activation;innate immune response
• Cellular component: extracellular region;integral component of membrane