ARPC4-TTLL3

ARPC4-TTLL3 readthrough

Basic information

Region (hg38): 3:9793082-9835401

Links

ENSG00000250151 ∙ NCBI:100526693 ∙ ∙ HGNC:38830 ∙ ∙ ∙ 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 ARPC4-TTLL3 gene.

• Inborn genetic diseases (33 variants)
• not provided (3 variants)
• Developmental delay, language impairment, and ocular abnormalities (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARPC4-TTLL3 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			1			1
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1		2	3
splice region						0
non coding			15			15
Total	0	0	25	0	2

Variants in ARPC4-TTLL3

This is a list of pathogenic ClinVar variants found in the ARPC4-TTLL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-9793135-C-G		Inborn genetic diseases	Uncertain significance (Oct 24, 2024)
3-9793135-C-T		Inborn genetic diseases	Uncertain significance (Apr 23, 2024)
3-9793138-G-C			Uncertain significance (May 08, 2024)
3-9793140-C-T		Inborn genetic diseases	Uncertain significance (Sep 29, 2023)
3-9793162-G-A		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
3-9797730-C-G		not specified	Uncertain significance (Oct 09, 2024)
3-9801666-T-G		Inborn genetic diseases	Uncertain significance (Oct 03, 2023)
3-9803849-G-A		Inborn genetic diseases	Uncertain significance (Aug 13, 2021)
3-9803984-C-T		Developmental delay, language impairment, and ocular abnormalities • Inborn genetic diseases	Conflicting classifications of pathogenicity (Mar 03, 2024)
3-9803987-A-G			Uncertain significance (Oct 11, 2023)
3-9810077-C-A		not specified	Uncertain significance (Dec 21, 2022)
3-9810110-A-C		not specified	Uncertain significance (Dec 14, 2023)
3-9810116-T-C		not specified	Likely benign (Oct 08, 2024)
3-9810124-C-G		not specified	Uncertain significance (Nov 21, 2022)
3-9810125-C-A		not specified	Uncertain significance (Nov 21, 2022)
3-9810136-G-A		not specified	Uncertain significance (Jun 12, 2023)
3-9810143-G-A		not specified	Uncertain significance (Jun 07, 2024)
3-9810179-G-T		not specified	Uncertain significance (May 20, 2024)
3-9810191-G-A		not specified	Uncertain significance (Oct 05, 2023)
3-9810244-G-A		not specified	Uncertain significance (Sep 14, 2022)
3-9810245-G-T		not specified	Uncertain significance (Jan 23, 2024)
3-9810266-C-G		not specified	Uncertain significance (Aug 27, 2024)
3-9810268-G-A		not specified	Uncertain significance (Dec 06, 2022)
3-9810283-C-T		not specified	Uncertain significance (Sep 16, 2021)
3-9810302-C-T		not specified	Uncertain significance (Aug 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARPC4-TTLL3	protein_coding	protein_coding	ENST00000397256	12	42320

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.36e-13	0.304	125596	0	152	125748	0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.998	334	389	0.858	0.0000240	4143
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00216	0.00215
Ashkenazi Jewish	0.00	0.00
East Asian	0.000599	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000666	0.000659
Middle Eastern	0.000599	0.000598
South Asian	0.000572	0.000555
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.67

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: protein polyglycylation;actin filament polymerization;Arp2/3 complex-mediated actin nucleation
• Cellular component: Arp2/3 protein complex
• Molecular function: protein-glycine ligase activity