SSC4D

protein-coding

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

Gene summary

The scavenger receptor cysteine-rich (SRCR) superfamily is an ancient and highly conserved group of cell surface and/or secreted proteins, some of which are involved in the development of the immune system and the regulation of both innate and adaptive immune responses. Group B SRCR domains usually contain 8 regularly spaced cysteines that give rise to a well-defined intradomain disulfide-bond pattern.[supplied by OMIM, Apr 2004]

Previous symbols:

SRCRB4D

MANE transcript

NM_080744.2

Inheritance

—

ClinVar variants

U:101B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr7:76,389,334-76,409,697

External References & Databases

Ensembl (ENSG00000146700)

Transcript & Mutation Effects

hg38 • Region Span ~20.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SSC4D variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 104

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080744.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			101 clinvar	5 clinvar		106
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	101	5	0	106

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080744.2	RefSeq	NP_542782.1	10	MANE Select
ENST00000275560.4	Ensembl	ENSP00000275560.3	10	MANE Select
ENST00000938539.1	Ensembl	ENSP00000608598.1	8	Standard
ENST00000938540.1	Ensembl	ENSP00000608599.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

receptor-mediated endocytosis

Molecular Function

scavenger receptor activity

Cellular Component

extracellular region
external side of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000275560
Coding exons: 10
Length: 20362
Individuals with no LoFs: 125657
Homozygous LoFs: 0
Heterozygous LoFs: 91
Defined: 125748
p: 0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.681	287	321	0.893	0.0000194	3577
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00052	0.00052	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0011	0.0011	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00014	rare
South Asian	0.0011	0.0011	notable
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.163

Intolerance Scores

RVIS EVS: 0.58
RVIS percentile EVS: 82.25

Essentials

Essential (gene trap): N