POM121

POM121 transmembrane nucleoporin, the group of Nucleoporins

Basic information

Region (hg38): 7:72879349-72951440

Links

ENSG00000196313 ∙ NCBI:9883 ∙ OMIM:615753 ∙ HGNC:19702 ∙ Uniprot:Q96HA1 ∙ 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 POM121 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POM121 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				4	1	5
missense			92	8	4	104
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	0	0	92	12	5

Variants in POM121

This is a list of pathogenic ClinVar variants found in the POM121 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-72925128-C-T			Likely benign (Dec 01, 2022)
7-72926426-C-G		not specified	Uncertain significance (Nov 30, 2022)
7-72926432-C-G		not specified	Uncertain significance (Dec 21, 2023)
7-72926449-C-T		not specified	Uncertain significance (Jun 09, 2022)
7-72926463-T-G		not specified	Likely benign (Jun 29, 2022)
7-72926848-G-A		not specified	Uncertain significance (May 24, 2024)
7-72926860-T-C		not specified	Uncertain significance (Jul 12, 2022)
7-72926923-G-A		not specified	Uncertain significance (Feb 11, 2022)
7-72926928-C-A		not specified	Uncertain significance (Nov 21, 2024)
7-72926937-C-A		not specified	Uncertain significance (Sep 24, 2024)
7-72926943-T-A		not specified	Uncertain significance (Dec 05, 2022)
7-72926960-G-T		not specified	Uncertain significance (Jun 09, 2022)
7-72928385-G-A		not specified	Likely benign (Mar 07, 2024)
7-72928387-G-A		not specified	Uncertain significance (Nov 08, 2024)
7-72928450-C-A		not specified	Uncertain significance (Feb 28, 2024)
7-72929945-G-C		not specified	Uncertain significance (Feb 03, 2022)
7-72929969-C-G		not specified	Uncertain significance (Dec 11, 2024)
7-72929969-C-T		not specified	Uncertain significance (Oct 25, 2024)
7-72930023-C-G		not specified	Uncertain significance (Oct 26, 2021)
7-72930034-G-A		not specified	Likely benign (Dec 12, 2024)
7-72930061-A-G		not specified	Uncertain significance (Mar 07, 2024)
7-72938593-T-C		not specified	Uncertain significance (Mar 19, 2024)
7-72938609-C-T		not specified	Uncertain significance (Jan 08, 2025)
7-72938635-G-A		not specified	Uncertain significance (Aug 19, 2024)
7-72938644-C-T		not specified	Uncertain significance (Dec 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POM121	protein_coding	protein_coding	ENST00000395270	12	72044

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0580	0.942	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.975	536	476	1.13	0.0000281	6274
Missense in Polyphen		129	132.26	0.97538		1948
Synonymous	-2.72	262	212	1.24	0.0000148	2207
Loss of Function	3.33	7	25.0	0.280	0.00000129	341

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.000111	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000272	0.000272
South Asian	0.000230	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential component of the nuclear pore complex (NPC). The repeat-containing domain may be involved in anchoring components of the pore complex to the pore membrane. When overexpressed in cells induces the formation of cytoplasmic annulate lamellae (AL). {ECO:0000269|PubMed:17900573}.
• Pathway: RNA transport - Homo sapiens (human);miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in squamous cell - TarBase;tRNA processing;Disease;Gene expression (Transcription);Regulation of HSF1-mediated heat shock response;Metabolism of carbohydrates;Rev-mediated nuclear export of HIV RNA;Late Phase of HIV Life Cycle;HIV Life Cycle;Interactions of Rev with host cellular proteins;Host Interactions of HIV factors;HIV Infection;snRNP Assembly;Vpr-mediated nuclear import of PICs;SUMOylation of DNA damage response and repair proteins;Transport of Ribonucleoproteins into the Host Nucleus;Viral Messenger RNA Synthesis;Export of Viral Ribonucleoproteins from Nucleus;SUMOylation of chromatin organization proteins;Influenza Viral RNA Transcription and Replication;Cellular responses to stress;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMOylation of DNA replication proteins;SUMO E3 ligases SUMOylate target proteins;NEP/NS2 Interacts with the Cellular Export Machinery;Metabolism of proteins;Influenza Life Cycle;Influenza Infection;Metabolism of RNA;Infectious disease;Metabolism;Transport of the SLBP independent Mature mRNA;Transport of the SLBP Dependant Mature mRNA;Transport of Mature mRNA Derived from an Intronless Transcript;Transport of Mature mRNAs Derived from Intronless Transcripts;SUMOylation;Cellular responses to external stimuli;Regulation of Glucokinase by Glucokinase Regulatory Protein;Glycolysis;Nuclear Pore Complex (NPC) Disassembly;tRNA processing in the nucleus;Transport of Mature mRNA derived from an Intron-Containing Transcript;Metabolism of non-coding RNA;Cellular response to heat stress;Nuclear Envelope Breakdown;Mitotic Prophase;M Phase;Nuclear import of Rev protein;Glucose metabolism;Transcriptional regulation by small RNAs;Cell Cycle;Interactions of Vpr with host cellular proteins;Cell Cycle, Mitotic;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.0865

Intolerance Scores

• loftool: 0.510
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.82

Haploinsufficiency Scores

• pHI: 0.226
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.268

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pom121

Gene ontology

• Biological process: mRNA export from nucleus;protein import into nucleus;viral process
• Cellular component: nuclear envelope;nuclear pore;nucleoplasm;endoplasmic reticulum membrane;integral component of membrane;nuclear membrane
• Molecular function: protein binding;nuclear localization sequence binding;structural constituent of nuclear pore