CD300LD

protein-coding

CD300 molecule like family member d, the group of V-set domain containing

Gene summary

Predicted to enable transmembrane signaling receptor activity and virus receptor activity. Predicted to be involved in immune response-activating signaling pathway. Predicted to act upstream of or within regulation of interleukin-6 production and regulation of tumor necrosis factor production. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2025]

MANE transcript

NM_001115152.2

Inheritance

—

ClinVar variants

U:29B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr17:74,579,365-74,592,283

External References & Databases

Ensembl (ENSG00000204345)

NCBI Gene (100131439)

Transcript & Mutation Effects

hg38 • Region Span ~12.9 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 CD300LD variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001115152.2. 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		1
missense			29 clinvar	2 clinvar		31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	3	0	32

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001115152.2	RefSeq	NP_001108624.1	4	MANE Select
ENST00000375352.1	Ensembl	ENSP00000364501.1	4	MANE Select
XM_047435046.1	RefSeq	XP_047291002.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Immune System
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Adaptive Immune System

Biological Process

immune system process
regulation of immune response

Molecular Function

protein binding

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375352
Coding exons: 4
Length: 12919
Individuals with no LoFs: 124916
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 124931
p: 0.0000600

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.119	98	101	0.967	0.00000499	1237
Missense (PolyPhen)		26	23.641	1.0998		305
Synonymous	-0.899	50	42.5	1.18	0.00000231	398
Loss of Function	0.324	8	9.05	0.884	4.53e-7	99

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00050	0.00049	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000027	rare
South Asian	0.000035	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.404
RVIS EVS: 0.31
RVIS percentile EVS: 72.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0940

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium