CRIM1

cysteine rich transmembrane BMP regulator 1, the group of Cysteine rich transmembrane BMP regulators

Basic information

Region (hg38): 2:36355778-36551135

Previous symbols: [ "S52" ]

Links

ENSG00000150938 ∙ NCBI:51232 ∙ OMIM:606189 ∙ HGNC:2359 ∙ Uniprot:Q9NZV1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• colobomatous macrophthalmia-microcornea syndrome (Supportive), mode of inheritance: AD
• colobomatous macrophthalmia-microcornea syndrome (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CRIM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRIM1 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				6	9	15
missense			56	8	4	68
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding					1	1
Total	0	0	57	14	14

Variants in CRIM1

This is a list of pathogenic ClinVar variants found in the CRIM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-36356299-T-G		not specified	Uncertain significance (Aug 17, 2021)
2-36356318-G-T		CRIM1-related disorder	Benign (Jun 26, 2019)
2-36356329-T-C		not specified	Uncertain significance (Sep 12, 2023)
2-36356357-G-T		not specified	Uncertain significance (Feb 28, 2023)
2-36356368-C-A		CRIM1-related disorder	Benign (Jul 01, 2019)
2-36356433-G-A			Likely benign (Mar 02, 2018)
2-36356582-A-G		not specified	Uncertain significance (Jul 26, 2022)
2-36356596-A-C		not specified	Uncertain significance (Apr 12, 2024)
2-36356616-T-C		CRIM1-related disorder	Benign (Dec 31, 2019)
2-36356620-G-C		not specified	Uncertain significance (Sep 22, 2023)
2-36356628-G-A		CRIM1-related disorder	Benign (Jul 13, 2018)
2-36396688-A-G		not specified	Uncertain significance (Sep 20, 2023)
2-36396719-G-A		not specified	Uncertain significance (Dec 02, 2022)
2-36441250-C-T		CRIM1-related disorder	Likely benign (Nov 06, 2019)
2-36441284-C-T		not specified	Uncertain significance (May 31, 2023)
2-36441350-C-G		not specified	Uncertain significance (Apr 16, 2024)
2-36441366-C-G		not specified	Uncertain significance (Aug 08, 2023)
2-36441430-C-T			Likely benign (May 15, 2018)
2-36441451-A-G		CRIM1-related disorder	Benign (Dec 31, 2019)
2-36441465-C-T		not specified	Uncertain significance (May 04, 2022)
2-36441495-A-C		not specified	Uncertain significance (Aug 21, 2023)
2-36442606-C-T		CRIM1-related disorder	Likely benign (Feb 26, 2020)
2-36442632-A-G		not specified	Uncertain significance (Jun 04, 2024)
2-36442638-G-A		not specified	Uncertain significance (Feb 08, 2023)
2-36442671-C-G		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRIM1	protein_coding	protein_coding	ENST00000280527	17	195210

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000286	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.194	587	600	0.978	0.0000349	6794
Missense in Polyphen		346	383.26	0.90278		4341
Synonymous	-2.84	291	235	1.24	0.0000147	1970
Loss of Function	5.75	6	49.8	0.120	0.00000237	612

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000707	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000341	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in CNS development by interacting with growth factors implicated in motor neuron differentiation and survival. May play a role in capillary formation and maintenance during angiogenesis. Modulates BMP activity by affecting its processing and delivery to the cell surface. {ECO:0000269|PubMed:12464430, ECO:0000269|PubMed:12805376}.
• Pathway: EGFR1 (Consensus)

Intolerance Scores

• loftool: 0.249
• rvis_EVS: -1.1
• rvis_percentile_EVS: 6.93

Haploinsufficiency Scores

• pHI: 0.264
• hipred: Y
• hipred_score: 0.605
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crim1
• Phenotype: limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; embryo phenotype; liver/biliary system phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); endocrine/exocrine gland phenotype; muscle phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of cell growth;nervous system development;negative regulation of endopeptidase activity;insulin-like growth factor receptor signaling pathway
• Cellular component: extracellular region;plasma membrane;integral component of membrane
• Molecular function: serine-type endopeptidase inhibitor activity;insulin-like growth factor-activated receptor activity;insulin-like growth factor binding;PDZ domain binding