CARMIL2 capping protein regulator and myosin 1 linker 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CARMIL2provided by HGNC
Official Full Name: capping protein regulator and myosin 1 linker 2provided by HGNC
Primary source: HGNC:HGNC:27089
See related: Ensembl:ENSG00000159753 MIM:610859; AllianceGenome:HGNC:27089
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: IMD58; RLTPR; LRRC16C; CARMIL2b
Summary: This gene encodes a member of the CARMIL (capping protein, Arp2/3, myosin-I linker) family of proteins. The encoded protein interacts with and negatively regulates the heterodimeric capping protein and promotes cell migration. Reduced expression of this gene has been observed in human psoriasis patients. Mutations in this gene cause a human immunodeficiency syndrome characterized by smooth muscle tumors and impaired T-cell function. [provided by RefSeq, May 2017]
Expression: Biased expression in lymph node (RPKM 12.2), spleen (RPKM 8.2) and 10 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q22.1

Exon count:: 39

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (67645144..67657569)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (73439913..73452337)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (67679047..67691472)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Human CARMIL2 deficiency underlies a broader immunological and clinical phenotype than CD28 deficiency.
Title: Human CARMIL2 deficiency underlies a broader immunological and clinical phenotype than CD28 deficiency.
Novel CARMIL2 loss-of-function variants are associated with pediatric inflammatory bowel disease.
Title: Novel CARMIL2 loss-of-function variants are associated with pediatric inflammatory bowel disease.
RLTPR Q575E: A novel recurrent gain-of-function mutation in patients with adult T-cell leukemia/lymphoma.
Title: RLTPR Q575E: A novel recurrent gain-of-function mutation in patients with adult T-cell leukemia/lymphoma.
A Novel Pathogenic Variant in CARMIL2 (RLTPR) Causing CARMIL2 Deficiency and EBV-Associated Smooth Muscle Tumors.
Title: A Novel Pathogenic Variant in CARMIL2 (RLTPR) Causing CARMIL2 Deficiency and EBV-Associated Smooth Muscle Tumors.
Synaptic actin stabilization protein loss in Down syndrome and Alzheimer disease.
Title: Synaptic actin stabilization protein loss in Down syndrome and Alzheimer disease.
Exogenous interleukin-2 can rescue in-vitro T cell activation and proliferation in patients with a novel capping protein regulator and myosin 1 linker 2 mutation.
Title: Exogenous interleukin-2 can rescue in-vitro T cell activation and proliferation in patients with a novel capping protein regulator and myosin 1 linker 2 mutation.
this study reports three patients with a recently described combined immunodeficiency disorder, CARMIL2-deficiency, bearing a novel homozygous mutation on splice-acceptor site region on CARMIL2-gene
Title: A Novel CARMIL2 Mutation Resulting in Combined Immunodeficiency Manifesting with Dermatitis, Fungal, and Viral Skin Infections As Well as Selective Antibody Deficiency.
This case provides evidence that CARMIL2 should be a candidate gene when diagnosing children with very early onset inflammatory and eosinophilic gastrointestinal disorders, even when signs of immunodeficiency are not observed.
Title: A Unique Presentation of Infantile-Onset Colitis and Eosinophilic Disease without Recurrent Infections Resulting from a Novel Homozygous CARMIL2 Variant.
The study highlights that human CARMIL2 deficiency can manifest with inflammatory bowel diseases (IBD)-like symptoms.
Title: CARMIL2 Deficiency Presenting as Very Early Onset Inflammatory Bowel Disease.
These cases showed that CARMIL2-deficiency is an autosomal recessive primary immunodeficiency disorder associated with defective CD28-mediated TCR co-signalling and impaired cytoskeletal dynamics.
Title: A human immunodeficiency syndrome caused by mutations in CARMIL2.

Submit: New GeneRIF Correction See all GeneRIFs (15)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Severe combined immunodeficiency due to CARMIL2 deficiency MedGen: C4748304 OMIM: 618131 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vif	vif	HIV Vif interacts with CARMIL2 (RLTPR)	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH64901 (e-PCR)
- UniSTS:89097

RH78775 (e-PCR)
- UniSTS:3597

RH68791 (e-PCR)
- UniSTS:30498

CTCF_3772 (e-PCR)
- UniSTS:462131

SHGC-61086 (e-PCR)
- UniSTS:59975

WI-21064 (e-PCR)
- UniSTS:72035

Ctcf (e-PCR), detects polymorphism
- UniSTS:141440

RH80821 (e-PCR)
- UniSTS:87978

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables phospholipid binding	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in actin filament network formation	IDA Inferred from Direct Assay more info	PubMed
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in establishment or maintenance of cell polarity	IDA Inferred from Direct Assay more info	PubMed
involved_in establishment or maintenance of monopolar cell polarity	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of barbed-end actin filament capping	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of extracellular matrix disassembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of lamellipodium assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of lamellipodium organization	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of ruffle assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of Arp2/3 complex-mediated actin nucleation	IBA Inferred from Biological aspect of Ancestor more info
involved_in wound healing, spreading of cells	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in actin cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
located_in cell leading edge	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in extrinsic component of cytoplasmic side of plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in intermediate filament cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
is_active_in lamellipodium	IBA Inferred from Biological aspect of Ancestor more info
located_in lamellipodium	IDA Inferred from Direct Assay more info	PubMed
located_in macropinosome	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in ruffle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: capping protein, Arp2/3 and myosin-I linker protein 2

Names: F-actin-uncapping protein RLTPR; RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing; RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein; leucine rich repeat containing 16C; leucine-rich repeat-containing protein 16C

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_054728.1 RefSeqGene

Range

5226..17651

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001013838.3 → NP_001013860.1 capping protein, Arp2/3 and myosin-I linker protein 2 isoform 1

See identical proteins and their annotated locations for NP_001013860.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) retains an intron in the 5' coding region and contains an alternate in-frame exon in the 3' coding region compared to variant 2. The encoded isoform (1, also known as CARMIL2a) has the same N- and C-termini but is longer compared to isoform 2.

Source sequence(s)

AB113647

Consensus CDS

CCDS45513.1

UniProtKB/Swiss-Prot

B8X2Z3, Q6F5E8

Related

ENSP00000334958.5, ENST00000334583.11

Conserved Domains (3) summary

cd00116
Location:277 → 644

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00034
Location:222 → 246

LRR_AMN1; leucine-rich repeat [structural motif]

pfam16000
Location:819 → 1109

CARMIL_C; CARMIL C-terminus
NM_001317026.3 → NP_001303955.1 capping protein, Arp2/3 and myosin-I linker protein 2 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) represents the shorter transcript and encodes the shorter isoform (2, also known as CARMIL2b).

Source sequence(s)

AB113647, FJ026014

Consensus CDS

CCDS81998.1

UniProtKB/Swiss-Prot

Q6F5E8

Related

ENSP00000441481.1, ENST00000545661.5

Conserved Domains (4) summary

cd00116
Location:277 → 608

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00033
Location:513 → 539

LRR_RI; leucine-rich repeat [structural motif]

sd00034
Location:222 → 246

LRR_AMN1; leucine-rich repeat [structural motif]

pfam16000
Location:783 → 1073

CARMIL_C; CARMIL C-terminus

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

67645144..67657569

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011522875.3 → XP_011521177.2 capping protein, Arp2/3 and myosin-I linker protein 2 isoform X1

UniProtKB/TrEMBL

A0A8Q3SII9

Related

ENSP00000512465.1, ENST00000696175.1
XM_017022953.2 → XP_016878442.1 capping protein, Arp2/3 and myosin-I linker protein 2 isoform X3

UniProtKB/TrEMBL

A0A8Q3SIB7

Related

ENSP00000512466.1, ENST00000696176.1
XM_011522874.2 → XP_011521176.1 capping protein, Arp2/3 and myosin-I linker protein 2 isoform X5

Conserved Domains (4) summary

cd00116
Location:282 → 613

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

sd00033
Location:491 → 517

LRR_RI; leucine-rich repeat [structural motif]

sd00034
Location:252 → 280

LRR_AMN1; leucine-rich repeat [structural motif]

pfam16000
Location:788 → 1078

CARMIL_C; CARMIL C-terminus
XM_047433644.1 → XP_047289600.1 capping protein, Arp2/3 and myosin-I linker protein 2 isoform X2
XM_047433645.1 → XP_047289601.1 capping protein, Arp2/3 and myosin-I linker protein 2 isoform X4

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

73439913..73452337

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054379646.1 → XP_054235621.1 capping protein, Arp2/3 and myosin-I linker protein 2 isoform X1
XM_054379648.1 → XP_054235623.1 capping protein, Arp2/3 and myosin-I linker protein 2 isoform X3
XM_054379650.1 → XP_054235625.1 capping protein, Arp2/3 and myosin-I linker protein 2 isoform X5
XM_054379647.1 → XP_054235622.1 capping protein, Arp2/3 and myosin-I linker protein 2 isoform X2
XM_054379649.1 → XP_054235624.1 capping protein, Arp2/3 and myosin-I linker protein 2 isoform X4