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.

• not_specified (160 variants)
• CRIM1-related_disorder (25 variants)
• not_provided (22 variants)

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. These statistics are base on transcript: NM_000016441.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			15	7	9	31
missense			171	12	4	187
nonsense			3			3
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)			8			8
Total	0	0	198	19	13

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
		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

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

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