CD300LD

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

Basic information

Region (hg38): 17:74579365-74592283

Links

ENSG00000204345 ∙ NCBI:100131439 ∙ OMIM:616301 ∙ HGNC:16848 ∙ Uniprot:Q6UXZ3 ∙ 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 CD300LD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD300LD 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				1		1
missense			10	1		11
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	11	2	0

Variants in CD300LD

This is a list of pathogenic ClinVar variants found in the CD300LD region.

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

Position	Type	Phenotype	Significance	ClinVar
17-74580099-C-T		not specified	Uncertain significance (Feb 12, 2024)
17-74582237-T-C		not specified	Uncertain significance (Dec 16, 2023)
17-74582281-G-T		not specified	Uncertain significance (Oct 22, 2021)
17-74582290-T-C		not specified	Uncertain significance (Sep 16, 2021)
17-74582311-C-T		not specified	Likely benign (Dec 18, 2023)
17-74588534-T-C		not specified	Uncertain significance (Jun 17, 2024)
17-74588605-C-T			Likely benign (Sep 01, 2022)
17-74588610-T-C		not specified	Uncertain significance (Mar 20, 2023)
17-74588662-C-A		not specified	Uncertain significance (Feb 28, 2025)
17-74588721-C-T		not specified	Uncertain significance (Dec 22, 2024)
17-74588723-G-C		not specified	Uncertain significance (Jan 14, 2025)
17-74588724-C-T		not specified	Uncertain significance (Oct 17, 2023)
17-74588735-C-T		not specified	Uncertain significance (Feb 13, 2025)
17-74588793-C-T		not specified	Uncertain significance (Mar 13, 2023)
17-74588835-C-T		not specified	Likely benign (Jan 16, 2025)
17-74592166-G-A		not specified	Uncertain significance (Dec 04, 2024)
17-74592213-C-T		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD300LD	protein_coding	protein_coding	ENST00000375352	4	12919

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000118	0.383	124916	0	15	124931	0.0000600

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.119	98	101	0.967	0.00000499	1237
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000130	0.000128
Ashkenazi Jewish	0.00	0.00
East Asian	0.000501	0.000494
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000265
Middle Eastern	0.000501	0.000494
South Asian	0.0000345	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

• loftool: 0.404
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd300ld5

Gene ontology

• Biological process: immune system process;regulation of immune response
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding