POM121L12

POM121 transmembrane nucleoporin like 12

Basic information

Region (hg38): 7:53035632-53036925

Links

ENSG00000221900 ∙ NCBI:285877 ∙ ∙ HGNC:25369 ∙ Uniprot:Q8N7R1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POM121L12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POM121L12 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in POM121L12

This is a list of pathogenic ClinVar variants found in the POM121L12 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-53035715-T-C		not specified	Uncertain significance (May 29, 2024)
7-53035717-T-A		not specified	Uncertain significance (Feb 06, 2024)
7-53035729-G-A		not specified	Uncertain significance (Jun 18, 2024)
7-53035744-G-A		not specified	Uncertain significance (Jan 30, 2024)
7-53035752-C-A		not specified	Uncertain significance (Sep 27, 2021)
7-53035756-C-G		not specified	Uncertain significance (Dec 30, 2023)
7-53035787-C-A		not specified	Uncertain significance (Jan 30, 2024)
7-53035879-C-T		not specified	Uncertain significance (Aug 17, 2021)
7-53035891-A-C		not specified	Uncertain significance (May 14, 2024)
7-53035919-C-A		not specified	Uncertain significance (Dec 05, 2022)
7-53035962-G-T		not specified	Uncertain significance (Sep 20, 2023)
7-53035963-A-G		not specified	Uncertain significance (Dec 28, 2023)
7-53035973-C-T		not specified	Uncertain significance (Aug 08, 2023)
7-53035985-A-G		not specified	Uncertain significance (Jan 08, 2024)
7-53036012-G-C		not specified	Uncertain significance (May 20, 2024)
7-53036036-G-T		not specified	Uncertain significance (Apr 25, 2022)
7-53036078-C-T		not specified	Uncertain significance (Oct 02, 2023)
7-53036149-C-A		not specified	Uncertain significance (Jul 06, 2021)
7-53036159-G-T		not specified	Uncertain significance (Oct 27, 2022)
7-53036171-A-G		not specified	Uncertain significance (Oct 12, 2022)
7-53036244-G-T		not specified	Uncertain significance (Dec 20, 2022)
7-53036269-G-A		not specified	Likely benign (Sep 01, 2021)
7-53036297-A-T		not specified	Uncertain significance (Mar 14, 2023)
7-53036322-C-A		not specified	Uncertain significance (Aug 12, 2021)
7-53036327-C-T		not specified	Uncertain significance (Jun 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POM121L12	protein_coding	protein_coding	ENST00000408890	1	1269

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.45	267	208	1.28	0.0000148	1850
Missense in Polyphen		106	82.562	1.2839		634
Synonymous	-2.61	129	96.4	1.34	0.00000740	653
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.696
• rvis_EVS: 1.47
• rvis_percentile_EVS: 95.25

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0555

Gene Damage Prediction

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

Gene ontology

• Biological process: protein import into nucleus
• Cellular component: nuclear pore
• Molecular function: nuclear localization sequence binding;structural constituent of nuclear pore