POM121L2

POM121 transmembrane nucleoporin like 2

Basic information

Region (hg38): 6:27285902-27312273

Links

ENSG00000158553 ∙ NCBI:94026 ∙ ∙ HGNC:13973 ∙ Uniprot:Q96KW2 ∙ 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 POM121L2 gene.

• Inborn genetic diseases (36 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POM121L2 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			33	4		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	5	0

Variants in POM121L2

This is a list of pathogenic ClinVar variants found in the POM121L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-27309073-T-C		not specified	Uncertain significance (May 09, 2023)
6-27309131-C-T		not specified	Likely benign (Jan 02, 2024)
6-27309133-C-T		not specified	Uncertain significance (Nov 08, 2021)
6-27309164-A-T		not specified	Uncertain significance (Dec 14, 2023)
6-27309203-G-C		not specified	Uncertain significance (Jan 08, 2024)
6-27309266-T-C		not specified	Uncertain significance (Jan 24, 2023)
6-27309277-G-A		not specified	Uncertain significance (Dec 14, 2023)
6-27309286-G-A		not specified	Uncertain significance (Feb 27, 2024)
6-27309287-C-T		not specified	Uncertain significance (Mar 06, 2023)
6-27309295-C-T		not specified	Uncertain significance (Oct 02, 2023)
6-27309304-C-G		not specified	Uncertain significance (Oct 12, 2022)
6-27309370-G-A			Likely benign (Oct 01, 2022)
6-27309478-A-T		not specified	Uncertain significance (Nov 30, 2022)
6-27309512-G-T		not specified	Uncertain significance (Aug 10, 2023)
6-27309642-G-T		not specified	Uncertain significance (Mar 14, 2023)
6-27309796-A-G		not specified	Likely benign (Dec 03, 2021)
6-27309877-G-A		not specified	Uncertain significance (Aug 22, 2023)
6-27309917-T-C		not specified	Uncertain significance (Aug 11, 2022)
6-27309959-A-G		not specified	Uncertain significance (Oct 05, 2022)
6-27310012-T-C		not specified	Uncertain significance (Jun 29, 2023)
6-27310145-C-T		not specified	Uncertain significance (Nov 30, 2022)
6-27310157-C-A		not specified	Uncertain significance (Dec 01, 2022)
6-27310157-C-T		not specified	Uncertain significance (Jun 11, 2021)
6-27310176-G-T		not specified	Uncertain significance (Feb 10, 2023)
6-27310223-T-C		not specified	Likely benign (Nov 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POM121L2	protein_coding	protein_coding	ENST00000444565	1	26268

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.327	0.499	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.16	396	537	0.738	0.0000257	6640
Missense in Polyphen		76	105.39	0.72111		1394
Synonymous	3.50	146	211	0.693	0.0000106	2301
Loss of Function	0.606	0	0.427	0.00	1.81e-8	5

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Pathway: RNA transport - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• pHI: 0.0337

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0445

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pom121l2

Gene ontology

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