SSC5D

protein-coding

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

Gene summary

Predicted to enable fibronectin binding activity; laminin binding activity; and scavenger receptor activity. Predicted to be involved in defense response; detection of bacterial lipoprotein; and negative regulation of interleukin-8 production. Predicted to act upstream of or within regulation of interleukin-8 production. Predicted to be located in cytoplasm; extracellular region; and membrane. Predicted to be active in extracellular matrix and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001144950.2

Inheritance

—

ClinVar variants

U:345B:39

Top phenotype

SSC5D-related disorder

gnomAD constraint

pLI —, LoF o/e 0.85

Max pathogenic AF

—

Genomic locus

chr19:55,488,404-55,519,099

External References & Databases

Ensembl (ENSG00000179954)

Transcript & Mutation Effects

hg38 • Region Span ~30.7 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 SSC5D variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 355

not providedTotal: 25

SSC5D-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001144950.2. 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			1 clinvar	17 clinvar	1 clinvar	19
missense			339 clinvar	21 clinvar		360
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	345	38	1	384

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001144950.2	RefSeq	NP_001138422.1	14	MANE Select
ENST00000389623.11	Ensembl	ENSP00000374274.4	14	MANE Select
NM_001195267.2	RefSeq	NP_001182196.1	13	Standard
ENST00000587166.5	Ensembl	ENSP00000467252.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Scavenging by Class B Receptors
Binding and Uptake of Ligands by Scavenger Receptors

Biological Process

receptor-mediated endocytosis
multicellular organism development
detection of bacterial lipoprotein
innate immune response
defense response to Gram-negative bacterium

Molecular Function

fibronectin binding
scavenger receptor activity
protein binding
laminin binding
extracellular matrix binding

Cellular Component

extracellular space
cytoplasm
external side of plasma membrane
collagen-containing extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389623
Coding exons: 14
Length: 30695
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.54	765	895	0.855	0.0000534	9845
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Intolerance Scores

RVIS EVS: 3.78
RVIS percentile EVS: 99.62

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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