CARMIL1

protein-coding

capping protein regulator and myosin 1 linker 1

Gene summary

Involved in several processes, including actin filament network formation; plasma membrane bounded cell projection organization; and positive regulation of cellular component organization. Located in several cellular components, including cytosol; lamellipodium; and macropinosome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

LRRC16
LRRC16A

MANE transcript

NM_017640.6

Inheritance

—

ClinVar variants

U:32

Top phenotype

Sensorineural hearing loss disorder

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr6:25,279,078-25,620,530

External References & Databases

Ensembl (ENSG00000079691)

Transcript & Mutation Effects

hg38 • Region Span ~341.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CARMIL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 8

Sensorineural hearing loss disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017640.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			7 clinvar			7
missense			17 clinvar			17
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	32	0	0	32

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017640.6	RefSeq	NP_060110.4	37	MANE Select
ENST00000329474.7	Ensembl	ENSP00000331983.6	37	MANE Select
NM_001173977.2	RefSeq	NP_001167448.1	37	Standard
ENST00000461945.1	Ensembl	ENSP00000489403.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Factors involved in megakaryocyte development and platelet production
Hemostasis

Biological Process

actin filament organization
blood coagulation
cell migration
lamellipodium assembly
positive regulation of cell migration

Molecular Function

protein binding
protein-containing complex binding

Cellular Component

nucleus
cytosol
plasma membrane
nuclear speck
lamellipodium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000329474
Coding exons: 37
Length: 341453
Individuals with no LoFs: 124608
Homozygous LoFs: 0
Heterozygous LoFs: 54
Defined: 124662
p: 0.000217

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.71	512	716	0.715	0.0000385	8902
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000068	0.000065	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00079	0.00080	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00023	0.00021	rare
South Asian	0.00048	0.00046	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0971

Intolerance Scores

RVIS EVS: -0.86
RVIS percentile EVS: 10.95

Essentials

Essential (gene trap): N