SSC4D

scavenger receptor cysteine rich family member with 4 domains, the group of Scavenger receptor cysteine rich domain containing|Scavenger receptors

Basic information

Region (hg38): 7:76389334-76409697

Previous symbols: [ "SRCRB4D" ]

Links

ENSG00000146700 ∙ NCBI:136853 ∙ OMIM:607639 ∙ HGNC:14461 ∙ Uniprot:Q8WTU2 ∙ 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 SSC4D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSC4D 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			40	3		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	3	0

Variants in SSC4D

This is a list of pathogenic ClinVar variants found in the SSC4D region.

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

Position	Type	Phenotype	Significance	ClinVar
7-76390066-G-A		not specified	Likely benign (Dec 21, 2023)
7-76390105-T-C		not specified	Uncertain significance (Apr 04, 2024)
7-76390253-G-A		not specified	Uncertain significance (Nov 20, 2024)
7-76390331-C-T		not specified	Uncertain significance (Oct 04, 2024)
7-76390340-C-T		not specified	Uncertain significance (Dec 17, 2023)
7-76390345-C-T		not specified	Uncertain significance (Oct 18, 2021)
7-76390372-T-C		not specified	Uncertain significance (May 12, 2024)
7-76391990-C-A		not specified	Uncertain significance (Oct 26, 2022)
7-76393443-T-C		not specified	Uncertain significance (Nov 10, 2022)
7-76393465-G-A		not specified	Uncertain significance (Jun 16, 2022)
7-76393528-C-A		not specified	Uncertain significance (Nov 23, 2024)
7-76393585-C-T		not specified	Uncertain significance (Oct 26, 2022)
7-76393671-C-T		not specified	Uncertain significance (Dec 23, 2022)
7-76393675-C-G		not specified	Uncertain significance (Nov 21, 2022)
7-76393677-C-G		not specified	Uncertain significance (Jun 29, 2023)
7-76393715-A-C		not specified	Uncertain significance (Oct 26, 2022)
7-76393850-G-A		not specified	Uncertain significance (Sep 27, 2021)
7-76393851-C-T		not specified	Uncertain significance (Aug 13, 2021)
7-76395259-G-A		not specified	Uncertain significance (Nov 13, 2023)
7-76395270-C-A		not specified	Uncertain significance (Jan 16, 2024)
7-76395289-T-C		not specified	Uncertain significance (Mar 19, 2024)
7-76395291-G-A		not specified	Uncertain significance (Aug 04, 2023)
7-76397674-C-G		not specified	Uncertain significance (Sep 30, 2021)
7-76397677-C-G		not specified	Uncertain significance (Sep 30, 2021)
7-76397679-A-C		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSC4D	protein_coding	protein_coding	ENST00000275560	10	20362

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.18e-12	0.200	125657	0	91	125748	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.681	287	321	0.893	0.0000194	3577
Missense in Polyphen		115	132.04	0.87093		1486
Synonymous	2.10	108	140	0.774	0.00000883	1220
Loss of Function	0.853	20	24.6	0.814	0.00000135	251

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000582	0.000582
Ashkenazi Jewish	0.00	0.00
East Asian	0.00109	0.00109
Finnish	0.00	0.00
European (Non-Finnish)	0.000149	0.000141
Middle Eastern	0.00109	0.00109
South Asian	0.00109	0.00108
Other	0.000495	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.163

Intolerance Scores

• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.25

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.300
• ghis: 0.415

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ssc4d

Gene ontology

• Biological process: receptor-mediated endocytosis
• Cellular component: extracellular region;external side of plasma membrane
• Molecular function: scavenger receptor activity