SSC5D

scavenger receptor cysteine rich family member with 5 domains, the group of Scavenger receptor cysteine rich domain containing|Scavenger receptors

Basic information

Region (hg38): 19:55488404-55519099

Links

ENSG00000179954 ∙ NCBI:284297 ∙ OMIM:618194 ∙ HGNC:26641 ∙ Uniprot:A1L4H1 ∙ 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 SSC5D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSC5D 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				11	1	12
missense			154	10	1	165
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	154	22	2

Variants in SSC5D

This is a list of pathogenic ClinVar variants found in the SSC5D region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55489062-G-GCC		SSC5D-related disorder	Likely benign (Nov 20, 2020)
19-55489377-C-T		not specified	Uncertain significance (Aug 28, 2023)
19-55489389-G-A		not specified	Uncertain significance (Jan 31, 2024)
19-55489395-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-55489398-C-G		not specified	Uncertain significance (May 05, 2023)
19-55489419-C-T		not specified	Uncertain significance (Nov 21, 2023)
19-55489431-G-A		not specified	Uncertain significance (Oct 29, 2024)
19-55489455-C-T		not specified	Uncertain significance (Feb 22, 2023)
19-55489461-G-A		not specified	Uncertain significance (Aug 19, 2023)
19-55489485-G-A		not specified	Uncertain significance (Jan 10, 2023)
19-55489491-G-A		not specified	Uncertain significance (Nov 10, 2022)
19-55489510-C-T		not specified	Uncertain significance (Jun 26, 2023)
19-55489518-G-A		not specified	Uncertain significance (May 03, 2023)
19-55489527-G-A		not specified	Uncertain significance (Mar 25, 2024)
19-55489550-G-T		not specified	Uncertain significance (Dec 03, 2024)
19-55489569-C-T		not specified	Uncertain significance (Aug 02, 2024)
19-55489570-G-A		not specified	Uncertain significance (Jun 18, 2021)
19-55489572-G-C		not specified	Uncertain significance (Dec 19, 2023)
19-55489605-C-T		not specified	Uncertain significance (Jan 26, 2022)
19-55489606-G-A		not specified	Uncertain significance (May 30, 2023)
19-55489635-G-A		not specified	Uncertain significance (Mar 31, 2024)
19-55489644-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-55489659-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-55489908-G-C		not specified	Uncertain significance (Dec 13, 2022)
19-55489927-A-G		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSC5D	protein_coding	protein_coding	ENST00000389623	14	30695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.16e-23	0.0125	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	765	895	0.855	0.0000534	9845
Missense in Polyphen		243	290.79	0.83567		3188
Synonymous	0.590	362	377	0.961	0.0000239	3599
Loss of Function	0.945	38	44.8	0.848	0.00000259	475

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to extracellular matrix proteins. Binds to pathogen-associated molecular patterns (PAMPs) present on the cell walls of Gram-positive and Gram-negative bacteria and fungi, behaving as a pattern recognition receptor (PRR). Induces bacterial and fungal aggregation and subsequent inhibition of PAMP-induced cytokine release. Does not possess intrinsic bactericidal activity. May play a role in the innate defense and homeostasis of certain epithelial surfaces (By similarity). {ECO:0000250}.
• Pathway: Vesicle-mediated transport;Scavenging by Class B Receptors;Binding and Uptake of Ligands by Scavenger Receptors (Consensus)

Intolerance Scores

• rvis_EVS: 3.78
• rvis_percentile_EVS: 99.62

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ssc5d

Gene ontology

• Biological process: receptor-mediated endocytosis;multicellular organism development;detection of bacterial lipoprotein;innate immune response;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;negative regulation of interleukin-8 secretion
• Cellular component: extracellular space;cytoplasm;external side of plasma membrane;collagen-containing extracellular matrix
• Molecular function: fibronectin binding;scavenger receptor activity;protein binding;laminin binding;extracellular matrix binding