CARMIL1

capping protein regulator and myosin 1 linker 1

Basic information

Region (hg38): 6:25279077-25620530

Previous symbols: [ "LRRC16", "LRRC16A" ]

Links

ENSG00000079691 ∙ NCBI:55604 ∙ OMIM:609593 ∙ HGNC:21581 ∙ Uniprot:Q5VZK9 ∙ 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 CARMIL1 gene.

• Inborn genetic diseases (5 variants)
• Sensorineural hearing loss disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CARMIL1 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						0
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in CARMIL1

This is a list of pathogenic ClinVar variants found in the CARMIL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-25279805-G-C		not specified	Uncertain significance (Jul 14, 2021)
6-25495134-C-A		not specified	Uncertain significance (Dec 08, 2023)
6-25539987-C-T		not specified	Uncertain significance (Oct 06, 2021)
6-25581284-A-G		not specified	Uncertain significance (Sep 16, 2021)
6-25600331-G-A		not specified	Uncertain significance (Jul 13, 2021)
6-25600439-G-A		Sensorineural hearing loss disorder	Uncertain significance (Sep 30, 2020)
6-25600522-G-A		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CARMIL1	protein_coding	protein_coding	ENST00000329474	37	341453

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0336	0.966	124608	0	54	124662	0.000217

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.71	512	716	0.715	0.0000385	8902
Missense in Polyphen		109	205.22	0.53113		2756
Synonymous	0.660	258	272	0.949	0.0000152	2604
Loss of Function	6.08	19	76.3	0.249	0.00000411	955

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000210
Ashkenazi Jewish	0.000795	0.000795
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000226	0.000212
Middle Eastern	0.00	0.00
South Asian	0.000476	0.000458
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell membrane-cytoskeleton-associated protein that plays a role in the regulation of actin polymerization at the barbed end of actin filaments. Prevents F-actin heterodimeric capping protein (CP) activity at the leading edges of migrating cells, and hence generates uncapped barbed ends and enhances actin polymerization, however, seems unable to nucleate filaments (PubMed:16054028). Plays a role in lamellipodial protrusion formations and cell migration (PubMed:19846667). {ECO:0000269|PubMed:16054028, ECO:0000269|PubMed:19846667}.
• Pathway: Factors involved in megakaryocyte development and platelet production;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.0971

Intolerance Scores

• rvis_EVS: -0.86
• rvis_percentile_EVS: 10.95

Haploinsufficiency Scores

• pHI: 0.278
• hipred: Y
• hipred_score: 0.526
• ghis: 0.522

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Carmil1
• Phenotype: normal phenotype

Gene ontology

• Biological process: actin filament organization;blood coagulation;cell migration;lamellipodium assembly;positive regulation of cell migration;positive regulation of actin filament polymerization;ruffle organization;macropinocytosis;urate metabolic process;positive regulation of stress fiber assembly;barbed-end actin filament uncapping;actin filament network formation;positive regulation of substrate adhesion-dependent cell spreading;positive regulation of lamellipodium organization;negative regulation of barbed-end actin filament capping
• Cellular component: nucleus;cytosol;plasma membrane;nuclear speck;lamellipodium;cell leading edge;filamentous actin;macropinosome;extracellular exosome
• Molecular function: protein binding;protein-containing complex binding