ALS2CL ALS2 C-terminal like [Homo sapiens (human)] - Gene

Summary

Official Symbol: ALS2CLprovided by HGNC
Official Full Name: ALS2 C-terminal likeprovided by HGNC
Primary source: HGNC:HGNC:20605
See related: Ensembl:ENSG00000178038 MIM:612402; AllianceGenome:HGNC:20605
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RN49018
Summary: Predicted to enable guanyl-nucleotide exchange factor activity and small GTPase binding activity. Predicted to be involved in endosomal transport. Predicted to act upstream of or within protein localization. Predicted to be located in cytosol. Predicted to be active in cytoplasmic vesicle. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in skin (RPKM 30.9), esophagus (RPKM 10.4) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p21.31

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (46668995..46693679, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (46685103..46709793, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (46710485..46735169, complement)

Chromosome 3 - NC_000003.12 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?

This supports the notion that de novo mutations in ALS2CL are extremely rare in schizophrenia
Title: Investigation of rare variants in LRP1, KPNA1, ALS2CL and ZNF480 genes in schizophrenia patients reflects genetic heterogeneity of the disease.
Data provide further support that ALS2CL, EPHA3, and CMYA1 are bona-fide tumor-suppressor genes and contribute to the tumorigenesis of HNSCC.
Title: Multiple tumor-suppressor genes on chromosome 3p contribute to head and neck squamous cell carcinoma tumorigenesis.
These results suggest that amyotrophic lateral sclerosis 2 C-terminal like (ALS2CL), a novel ALS2 homologue, modulates Rab5-mediated endosome dynamics in HeLa cells.
Title: ALS2CL, the novel protein highly homologous to the carboxy-terminal half of ALS2, binds to Rab5 and modulates endosome dynamics.
ALS2CL is a novel ALS2-interacting protein implicated in ALS2-mediated endosome dynamics.
Title: ALS2CL, a novel ALS2-interactor, modulates ALS2-mediated endosome dynamics.

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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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-147558 (e-PCR)
- UniSTS:175875

STS-N49393 (e-PCR)
- UniSTS:29971

RH98898 (e-PCR)
- UniSTS:87087

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase activator activity	IEA Inferred from Electronic Annotation more info
enables guanyl-nucleotide exchange factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in endosomal transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasmic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	TAS Traceable Author Statement more info

General protein information

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Preferred Names: ALS2 C-terminal-like protein

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.

mRNA and Protein(s)

NM_001190707.2 → NP_001177636.1 ALS2 C-terminal-like protein isoform 1

See identical proteins and their annotated locations for NP_001177636.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).

Source sequence(s)

AC134504, AK126505, AK131270, DA242202, DB350037

Consensus CDS

CCDS2743.1

UniProtKB/Swiss-Prot

Q32MA1, Q60I27, Q6AI56, Q6ZNC5, Q6ZNC7, Q6ZTL4, Q86YD2, Q8N9U1, Q8NAL7

Related

ENSP00000413223.1, ENST00000415953.5

Conserved Domains (4) summary

COG4642
Location:358 → 519

COG4642; Uncharacterized conserved protein [Function unknown]

pfam02204
Location:834 → 938

VPS9; Vacuolar sorting protein 9 (VPS9) domain

pfam02493
Location:358 → 378

MORN; MORN repeat

cl17171
Location:223 → 321

PH-like; Pleckstrin homology-like domain
NM_147129.5 → NP_667340.2 ALS2 C-terminal-like protein isoform 1

See identical proteins and their annotated locations for NP_667340.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the same isoform (1) as variant 2.

Source sequence(s)

AB107015, AC134504, AK126505, DB350037

Consensus CDS

CCDS2743.1

UniProtKB/Swiss-Prot

Q32MA1, Q60I27, Q6AI56, Q6ZNC5, Q6ZNC7, Q6ZTL4, Q86YD2, Q8N9U1, Q8NAL7

Related

ENSP00000313670.4, ENST00000318962.9

Conserved Domains (4) summary

COG4642
Location:358 → 519

COG4642; Uncharacterized conserved protein [Function unknown]

pfam02204
Location:834 → 938

VPS9; Vacuolar sorting protein 9 (VPS9) domain

pfam02493
Location:358 → 378

MORN; MORN repeat

cl17171
Location:223 → 321

PH-like; Pleckstrin homology-like domain

RNA

NR_033815.3 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC134504, AK126505, AL832132, DB350037
NR_135622.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC104304, AC134504

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

46668995..46693679 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

46685103..46709793 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_182774.1: Suppressed sequence

Description

NM_182774.1: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.
NM_182775.2: Suppressed sequence

Description

NM_182775.2: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.