NMS

protein-coding

neuromedin S, the group of Neuropeptides

Gene summary

This gene encodes a member of the neuromedin family of neuropeptides. The encoded preproprotein is proteolytically processed to generate a biologically active neuropeptide that plays a role in the regulation of circadian rhythm, anorexigenic action, antidiuretic action, cardiovascular function and stimulation of oxytocin and vasopressin release. [provided by RefSeq, May 2016]

MANE transcript

NM_001011717.1

Inheritance

—

ClinVar variants

U:18B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.08

Max pathogenic AF

—

Genomic locus

chr2:100,470,482-100,483,280

External References & Databases

Ensembl (ENSG00000204640)

Transcript & Mutation Effects

hg38 • Region Span ~12.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NMS variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 20

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001011717.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			18 clinvar	2 clinvar		20
nonsense						0
start loss					1 clinvar	1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	18	2	1	21

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001011717.1	RefSeq	NP_001011717.1	10	MANE Select
ENST00000376865.1	Ensembl	ENSP00000366061.1	10	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling by GPCR
Signal Transduction
Peptide ligand-binding receptors
Class A/1 (Rhodopsin-like receptors)
GPCR ligand binding

Biological Process

G protein-coupled receptor signaling pathway
neuropeptide signaling pathway
locomotor rhythm

Molecular Function

G protein-coupled receptor binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376865
Coding exons: 10
Length: 12799
Individuals with no LoFs: 125679
Homozygous LoFs: 0
Heterozygous LoFs: 67
Defined: 125746
p: 0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0626	84	82.4	1.02	0.00000425	990
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.0017	0.0017	notable
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Implicated in the regulation of circadian rhythms through autocrine and/or paracrine actions. {ECO:0000250}.;

Recessive Scores

pRec: 0.129

Intolerance Scores

LoFtool: 0.788
RVIS EVS: 0.26
RVIS percentile EVS: 70.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.314

Gene Damage Prediction

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