CLGN

calmegin

Basic information

Region (hg38): 4:140388453-140427661

Links

ENSG00000153132 ∙ NCBI:1047 ∙ OMIM:601858 ∙ HGNC:2060 ∙ Uniprot:O14967 ∙ 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 CLGN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLGN 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			31	2		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	1

Variants in CLGN

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

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

Position	Type	Phenotype	Significance	ClinVar
4-140389234-C-T		not specified	Uncertain significance (Mar 02, 2023)
4-140389249-C-T		not specified	Uncertain significance (Aug 24, 2023)
4-140390662-C-T		not specified	Uncertain significance (Jan 10, 2023)
4-140390720-T-C		not specified	Likely benign (Mar 27, 2023)
4-140392233-T-G		not specified	Uncertain significance (Jan 10, 2023)
4-140392267-C-A		not specified	Uncertain significance (Nov 03, 2023)
4-140392285-C-T		not specified	Uncertain significance (Nov 03, 2023)
4-140392350-T-G		not specified	Uncertain significance (Feb 27, 2024)
4-140392621-A-C		not specified	Uncertain significance (May 20, 2024)
4-140393863-C-T		not specified	Uncertain significance (Jul 12, 2023)
4-140393882-C-A		not specified	Uncertain significance (Aug 09, 2021)
4-140393899-G-A		not specified	Uncertain significance (Aug 22, 2023)
4-140393957-C-A		not specified	Uncertain significance (Jan 16, 2024)
4-140394031-C-T		not specified	Uncertain significance (Aug 26, 2022)
4-140395849-T-A		not specified	Uncertain significance (Jan 02, 2024)
4-140395883-A-T		not specified	Uncertain significance (Jan 24, 2023)
4-140396099-C-T		not specified	Uncertain significance (Dec 28, 2023)
4-140396120-C-G		not specified	Uncertain significance (Nov 07, 2022)
4-140396120-C-T		not specified	Uncertain significance (Oct 05, 2023)
4-140396131-T-C		Short stature	Likely pathogenic (Nov 18, 2001)
4-140398867-C-A		not specified	Uncertain significance (Mar 20, 2024)
4-140398987-T-C		not specified	Uncertain significance (Mar 07, 2023)
4-140399004-T-C		Short stature • not specified	Uncertain significance (Oct 28, 2023)
4-140400423-C-T		not specified	Uncertain significance (Aug 17, 2022)
4-140400465-T-C		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLGN	protein_coding	protein_coding	ENST00000325617	14	39514

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.28e-11	0.765	125638	0	102	125740	0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.789	270	309	0.874	0.0000142	4075
Missense in Polyphen		64	86.07	0.74358		1135
Synonymous	0.169	99	101	0.979	0.00000501	1040
Loss of Function	1.67	22	32.2	0.683	0.00000136	436

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00183	0.00182
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000438	0.000431
Middle Eastern	0.000220	0.000217
South Asian	0.000298	0.000294
Other	0.000332	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions during spermatogenesis as a chaperone for a range of client proteins that are important for sperm adhesion onto the egg zona pellucida and for subsequent penetration of the zona pellucida. Required for normal sperm migration from the uterus into the oviduct. Required for normal male fertility. Binds calcium ions (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.977
• rvis_EVS: 0.56
• rvis_percentile_EVS: 81.63

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.267
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.832

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clgn
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: protein folding;single fertilization;binding of sperm to zona pellucida;protein-containing complex assembly
• Cellular component: nuclear envelope;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: calcium ion binding;protein folding chaperone;unfolded protein binding