NEMP1

nuclear envelope integral membrane protein 1

Basic information

Region (hg38): 12:57055642-57088063

Previous symbols: [ "TMEM194", "TMEM194A" ]

Links

ENSG00000166881 ∙ NCBI:23306 ∙ OMIM:616496 ∙ HGNC:29001 ∙ Uniprot:O14524 ∙ 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 NEMP1 gene.

• Inborn genetic diseases (16 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEMP1 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			15	1	2	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	2

Variants in NEMP1

This is a list of pathogenic ClinVar variants found in the NEMP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57059916-C-T			Benign (May 14, 2018)
12-57059963-A-C		not specified	Uncertain significance (Feb 01, 2023)
12-57059977-T-C		not specified	Uncertain significance (Jan 03, 2024)
12-57060790-C-T		not specified	Uncertain significance (Dec 06, 2021)
12-57060797-C-G		not specified	Uncertain significance (Jan 08, 2024)
12-57060859-C-T		not specified	Likely benign (Jul 05, 2023)
12-57060869-C-T		not specified	Uncertain significance (Aug 22, 2023)
12-57060917-C-G		not specified	Uncertain significance (Aug 15, 2023)
12-57060937-C-G			Benign (Jul 16, 2018)
12-57063170-A-G		not specified	Uncertain significance (Jan 24, 2024)
12-57063176-A-G		not specified	Uncertain significance (Oct 06, 2022)
12-57063275-C-T		not specified	Uncertain significance (Aug 28, 2023)
12-57063278-T-C		not specified	Uncertain significance (May 24, 2023)
12-57063330-C-G		not specified	Uncertain significance (Feb 01, 2023)
12-57064131-T-G		not specified	Uncertain significance (Sep 29, 2023)
12-57064717-T-C		not specified	Uncertain significance (Apr 25, 2022)
12-57069252-C-T		not specified	Uncertain significance (Oct 05, 2023)
12-57072892-C-G		not specified	Uncertain significance (Dec 19, 2022)
12-57072895-C-A		not specified	Uncertain significance (Feb 22, 2023)
12-57078655-G-A		not specified	Uncertain significance (Oct 17, 2023)
12-57078660-C-G		not specified	Uncertain significance (Sep 26, 2023)
12-57078673-C-T		not specified	Uncertain significance (Feb 10, 2022)
12-57078679-C-G		not specified	Uncertain significance (Nov 17, 2022)
12-57078697-G-A		not specified	Uncertain significance (Jul 19, 2022)
12-57078714-G-A		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEMP1	protein_coding	protein_coding	ENST00000300128	9	32421

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.916	0.0838	125737	0	6	125743	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	187	233	0.802	0.0000115	2876
Missense in Polyphen		76	95.862	0.79281		1255
Synonymous	-0.148	88	86.3	1.02	0.00000394	869
Loss of Function	3.95	4	25.6	0.156	0.00000157	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000180	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000659	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.23

Haploinsufficiency Scores

• pHI: 0.272
• hipred: N
• hipred_score: 0.368
• ghis: 0.460

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Nemp1

Gene ontology

• Biological process: biological_process
• Cellular component: nuclear envelope;nuclear inner membrane;integral component of membrane
• Molecular function: molecular_function