ARPC4-TTLL3

protein-coding

ARPC4-TTLL3 readthrough

Gene summary

This locus represents naturally occurring read-through transcription between the neighboring ARPC4 (actin related protein 2/3 complex, subunit 4) and TTLL3 (tubulin tyrosine ligase-like family, member 3) genes. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]

MANE transcript

N/A

Inheritance

—

ClinVar variants

U:10B:2

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr3:9,793,082-9,835,401

External References & Databases

Ensembl (ENSG00000250151)

NCBI Gene (100526693)

HGNC:38830

GenCC

ClinVar (ARPC4-TTLL3)

Transcript & Mutation Effects

hg38 • Region Span ~42.3 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 ARPC4-TTLL3 variants in ClinVar

3 Conditions Cataloged

Inborn genetic diseasesTotal: 33

not providedTotal: 3

Developmental delay, language impairment, and ocular abnormalitiesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . 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			1 clinvar			1
missense			8 clinvar			8
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar		2 clinvar	3
Total	0	0	10	0	2	12

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001198793.1	RefSeq	NP_001185722.1	12	Standard
ENST00000397256.5	Ensembl	ENSP00000380427.1	12	Standard
ENST00000418163.5	Ensembl	ENSP00000402163.1	3	Standard
ENST00000424442.5	Ensembl	ENSP00000412284.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein polyglycylation
actin filament polymerization
Arp2/3 complex-mediated actin nucleation

Molecular Function

protein-glycine ligase activity

Cellular Component

Arp2/3 protein complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397256
Coding exons: 12
Length: 42320
Individuals with no LoFs: 125596
Homozygous LoFs: 0
Heterozygous LoFs: 152
Defined: 125748
p: 0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.998	334	389	0.858	0.0000240	4143
Missense (PolyPhen)		81	123.2	0.65747		1192
Synonymous	1.45	130	153	0.851	0.00000960	1196
Loss of Function	1.21	24	31.3	0.766	0.00000169	330

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0016	0.0016	notable
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00060	0.00060	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00067	0.00066	rare
South Asian	0.00057	0.00056	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.71
RVIS percentile EVS: 14.67

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	High	Medium	High