SUSD6

sushi domain containing 6, the group of Sushi domain containing

Basic information

Region (hg38): 14:69611596-69715144

Previous symbols: [ "KIAA0247" ]

Links

ENSG00000100647 ∙ NCBI:9766 ∙ OMIM:616761 ∙ HGNC:19956 ∙ Uniprot:Q92537 ∙ 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 SUSD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUSD6 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				1		1
missense			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	0

Variants in SUSD6

This is a list of pathogenic ClinVar variants found in the SUSD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-69658600-A-G		not specified	Uncertain significance (Aug 29, 2022)
14-69658611-G-A		not specified	Uncertain significance (Sep 20, 2023)
14-69658638-G-A		not specified	Uncertain significance (Aug 01, 2022)
14-69658659-G-A		not specified	Uncertain significance (Nov 08, 2024)
14-69658668-C-G		not specified	Uncertain significance (Oct 03, 2023)
14-69658700-C-T		not specified	Likely benign (Dec 17, 2023)
14-69658707-G-A		not specified	Uncertain significance (Nov 26, 2024)
14-69703410-C-T		not specified	Uncertain significance (Mar 10, 2025)
14-69703433-A-G		not specified	Uncertain significance (Mar 04, 2024)
14-69703445-C-T		not specified	Uncertain significance (Jul 02, 2024)
14-69703566-T-C		not specified	Uncertain significance (Dec 03, 2024)
14-69703587-A-G		not specified	Uncertain significance (Jun 29, 2023)
14-69704611-C-A		not specified	Uncertain significance (Oct 05, 2021)
14-69704669-G-A		not specified	Uncertain significance (Jan 18, 2025)
14-69704687-C-G		not specified	Uncertain significance (Nov 09, 2021)
14-69704735-C-T		not specified	Uncertain significance (Jun 29, 2022)
14-69708687-G-T		not specified	Uncertain significance (Dec 08, 2021)
14-69708715-T-C		not specified	Uncertain significance (May 15, 2023)
14-69708720-G-A		not specified	Uncertain significance (May 31, 2022)
14-69708765-G-A		not specified	Uncertain significance (Jan 17, 2025)
14-69708804-G-A		not specified	Uncertain significance (Jun 07, 2023)
14-69708811-T-C		not specified	Uncertain significance (Feb 13, 2024)
14-69708832-G-A		not specified	Uncertain significance (Jan 31, 2023)
14-69708849-G-T		not specified	Uncertain significance (Apr 22, 2022)
14-69708882-G-T		not specified	Uncertain significance (Jul 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUSD6	protein_coding	protein_coding	ENST00000342745	5	103547

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.633	0.366	125730	0	12	125742	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.521	160	180	0.891	0.0000101	1928
Missense in Polyphen		54	66.412	0.8131		764
Synonymous	-0.171	82	80.1	1.02	0.00000504	660
Loss of Function	2.65	2	11.8	0.169	5.01e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000358	0.0000352
Middle Eastern	0.0000550	0.0000544
South Asian	0.000103	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in growth-suppressive activity and cell death (PubMed:24652652). May be involved in the production of chemokine molecules in umbilical vein endothelial cells (HUVECs) cultured in THP1 monocyte LPS-induced medium (PubMed:20236627). Plays a role in preventing tumor onset (By similarity). {ECO:0000250|UniProtKB:Q8BGE4, ECO:0000269|PubMed:20236627, ECO:0000269|PubMed:24652652}.

Recessive Scores

• pRec: 0.0937

Intolerance Scores

• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.115
• hipred: Y
• hipred_score: 0.595
• ghis: 0.501

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Susd6
• Phenotype: normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: cellular response to DNA damage stimulus;cell death
• Cellular component: cellular_component;integral component of membrane
• Molecular function: molecular_function;protein binding