NMS

neuromedin S, the group of Neuropeptides

Basic information

Region (hg38): 2:100470481-100483280

Links

ENSG00000204640 ∙ NCBI:129521 ∙ OMIM:619337 ∙ HGNC:32203 ∙ Uniprot:Q5H8A3 ∙ 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 NMS gene.

• Inborn genetic diseases (5 variants)
• not provided (1 variants)

Variants pathogenicity by type

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

Variants in NMS

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

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

Position	Type	Phenotype	Significance	ClinVar
2-100470489-A-G			Benign (Aug 22, 2018)
2-100470544-T-C		not specified	Uncertain significance (May 17, 2023)
2-100472798-T-C		not specified	Uncertain significance (Mar 02, 2023)
2-100473528-C-T		not specified	Uncertain significance (Dec 13, 2022)
2-100477404-T-C		not specified	Uncertain significance (Jun 02, 2023)
2-100481136-C-T		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NMS	protein_coding	protein_coding	ENST00000376865	10	12799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.33e-11	0.0274	125679	0	67	125746	0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0626	84	82.4	1.02	0.00000425	990
Missense in Polyphen		10	11.276	0.88683		152
Synonymous	-1.13	33	25.7	1.28	0.00000126	271
Loss of Function	-0.298	16	14.8	1.08	8.07e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000880	0.0000880
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.000219	0.000217
South Asian	0.00169	0.00167
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Implicated in the regulation of circadian rhythms through autocrine and/or paracrine actions. {ECO:0000250}.
• Pathway: Signaling by GPCR;Signal Transduction;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;G alpha (q) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.788
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.0817
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.314

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nms

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;locomotor rhythm
• Cellular component: extracellular region
• Molecular function: G protein-coupled receptor binding