CRELD2

cysteine rich with EGF like domains 2

Basic information

Region (hg38): 22:49918167-49927540

Links

ENSG00000184164 ∙ NCBI:79174 ∙ OMIM:607171 ∙ HGNC:28150 ∙ Uniprot:Q6UXH1 ∙ 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 CRELD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRELD2 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				3	2	5
missense			54	2		56
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	54	5	3

Variants in CRELD2

This is a list of pathogenic ClinVar variants found in the CRELD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-49918260-G-A		ALG12-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
22-49918325-A-G		ALG12-congenital disorder of glycosylation	Benign (Jan 13, 2018)
22-49918341-AAC-A		Congenital disorder of glycosylation	Likely benign (Jun 14, 2016)
22-49918387-C-G		ALG12-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
22-49918387-C-T		ALG12-congenital disorder of glycosylation	Benign (Jan 13, 2018)
22-49918415-A-C		ALG12-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
22-49918782-C-T		not specified	Uncertain significance (Apr 04, 2023)
22-49918786-G-A		not specified	Uncertain significance (Dec 28, 2024)
22-49918809-C-T		not specified	Uncertain significance (Jul 13, 2021)
22-49918834-C-T		not specified	Uncertain significance (Dec 01, 2022)
22-49918866-C-G		not specified	Uncertain significance (May 03, 2023)
22-49918866-C-T		not specified	Uncertain significance (Apr 08, 2024)
22-49918867-G-A		not specified	Uncertain significance (May 16, 2022)
22-49918881-G-C		not specified	Uncertain significance (Nov 06, 2023)
22-49919266-G-A		not specified	Uncertain significance (Dec 16, 2024)
22-49919731-G-A		not specified	Uncertain significance (Jan 17, 2023)
22-49919792-A-G		not specified	Uncertain significance (Mar 16, 2022)
22-49919793-G-C		not specified	Uncertain significance (Jun 13, 2022)
22-49920160-A-G		not specified	Uncertain significance (Jul 27, 2024)
22-49920186-G-T		not specified	Uncertain significance (May 31, 2023)
22-49920232-G-A		not specified	Uncertain significance (Dec 24, 2024)
22-49920232-G-C		not specified	Uncertain significance (Sep 10, 2024)
22-49920232-G-T		not specified	Uncertain significance (Jan 10, 2023)
22-49921599-T-C		not specified	Uncertain significance (Aug 17, 2022)
22-49921617-G-A		not specified	Uncertain significance (Mar 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRELD2	protein_coding	protein_coding	ENST00000404488	11	9374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.79e-8	0.745	99501	1728	24468	125697	0.110

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.419	221	239	0.924	0.0000156	2581
Missense in Polyphen		83	101.07	0.82122		1120
Synonymous	-0.128	108	106	1.02	0.00000879	741
Loss of Function	1.38	15	22.0	0.683	9.38e-7	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.393	0.322
Ashkenazi Jewish	0.120	0.113
East Asian	0.0584	0.0535
Finnish	0.109	0.104
European (Non-Finnish)	0.112	0.104
Middle Eastern	0.0584	0.0535
South Asian	0.165	0.149
Other	0.117	0.105

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate transport of alpha4-beta2 neuronal acetylcholine receptor.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.259
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.66

Haploinsufficiency Scores

• pHI: 0.237
• hipred: N
• hipred_score: 0.144
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.486

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Creld2
• Phenotype: reproductive system phenotype

Gene ontology

• Cellular component: extracellular space;endoplasmic reticulum;Golgi apparatus
• Molecular function: calcium ion binding;protein binding