PIERCE1

piercer of microtubule wall 1

Basic information

Region (hg38): 9:135495180-135501734

Previous symbols: [ "C9orf116" ]

Links

ENSG00000160345 ∙ NCBI:138162 ∙ OMIM:614502 ∙ HGNC:28435 ∙ Uniprot:Q5BN46 ∙ AlphaFold ∙ 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 PIERCE1 gene.

• not provided (8 variants)
• Inborn genetic diseases (6 variants)
• Combined oxidative phosphorylation deficiency 36 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIERCE1 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8	3	2	13
Total	0	0	8	3	2

Variants in PIERCE1

This is a list of pathogenic ClinVar variants found in the PIERCE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-135495543-G-T		not specified	Uncertain significance (Jul 26, 2021)
9-135499835-G-A		not specified	Uncertain significance (Jun 21, 2021)
9-135500724-C-T		Combined oxidative phosphorylation deficiency 36	Uncertain significance (Aug 14, 2023)
9-135500735-C-A		not specified	Uncertain significance (Aug 02, 2021)
9-135500735-C-T		not specified	Uncertain significance (Jul 11, 2022)
9-135500755-TGAGC-T			Uncertain significance (Dec 11, 2023)
9-135500987-C-G			Uncertain significance (Jun 14, 2023)
9-135500990-C-A			Likely benign (Dec 07, 2023)
9-135501000-G-A			Uncertain significance (Nov 04, 2023)
9-135501019-G-A			Uncertain significance (Jun 06, 2023)
9-135501025-G-A		not specified	Uncertain significance (Oct 23, 2023)
9-135501026-C-G			Likely benign (Jun 12, 2023)
9-135501043-C-A		MRPS2-related disorder	Benign (Jan 29, 2024)
9-135501047-C-T			Likely benign (Nov 10, 2023)
9-135501050-G-A			Likely benign (Jul 14, 2023)
9-135501058-G-T		not specified	Uncertain significance (Feb 13, 2023)
9-135501066-C-G		not specified	Likely benign (Sep 12, 2023)
9-135501094-T-A		MRPS2-related disorder • not specified	Conflicting classifications of pathogenicity (Jan 26, 2023)
9-135501109-C-T			Benign (Jun 22, 2023)
9-135501132-G-A		MRPS2-related disorder	Likely benign (Jan 13, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIERCE1	protein_coding	protein_coding	ENST00000429260	3	6554

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000227	0.171	125707	0	27	125734	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.534	69	82.7	0.835	0.00000463	888
Missense in Polyphen		22	28.596	0.76934		316
Synonymous	-0.681	43	37.7	1.14	0.00000241	260
Loss of Function	-0.852	6	4.13	1.45	1.76e-7	48

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000251	0.000251
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000146	0.000141
Middle Eastern	0.00	0.00
South Asian	0.0000343	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.293
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.201
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 1700007K13Rik
• Phenotype: digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; embryo phenotype; respiratory system phenotype; liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: cellular response to DNA damage stimulus;determination of left/right symmetry;regulation of gene expression;cellular response to UV-C
• Cellular component: nucleus
• Molecular function: protein binding