View genomic variant #0000000006

Chromosome 1
Allele Unknown
Affects function (as reported) Affects function
Affects function (by curator) Affects function
Type subst
DNA change (genomic) (Relative to hg19 / GRCh37) g.10042688G>A
Published as -
GERP 5.010
Segregation -
DB-ID NMNAT1_000002
MSCV MSCV_0010006
dbSNP ID rs150726175
Frequency -
Sources ; clinvar; ensembl;
Reference 22842231;22842229;20301475;22842227;22842230
Variant remarks -
Genetic origin -
Variant_disease -
Average frequency (large NGS studies) 0.00108 View details
Owner LOVD

Variant on transcripts

2 entries on 1 page. Showing entries 1 - 2.


Transcript ID     


Variant ID     

Affects function     

DNA change (cDNA)     


GVS function     




RNA change     

NMNAT1 00003156 NM_022787.3 0000000006 +/+ c.769G>A p.(Glu257Lys) missense_variant - 5/5 benign(0.037) r.(?) tolerated(0.24)
NMNAT1 00003345 XR_244792.1 0000000006 +/+ n.866G>A - - - - - - -

ClinVar @ MSeqDR

RCVaccession RCV000030765; RCV000255806; RCV000504859; RCV001003567; RCV001075816;
Chromosome 1:10042688..10042688
Allele frequencies from ESP 0.00108
Allele frequencies from ExAC 0.00061
Allele frequencies from TGP 0.00020
ClinVar Allele ID 45795
Disease database name and identifier Human Phenotype Ontology:HP:0000556, Human Phenotype Ontology:HP:0007736, Human Phenotype Ontology:HP:0007910, Human Phenotype Ontology:HP:0007974, Human Phenotype Ontology:HP:0007982, MONDO:MONDO:0019118, MeSH:D058499, MedGen:C0854723, Orphanet:71862|Human Phenotype Ontology:HP:0002014, MedGen:C0011991|Human Phenotype Ontology:HP:0000639, MONDO:MONDO:0004843, MedGen:C0028738|Human Phenotype Ontology:HP:0001141, Human Phenotype Ontology:HP:0007640, Human Phenotype Ontology:HP:0007842, Human Phenotype Ontology:HP:0007951, Human Phenotype Ontology:HP:0008023, MedGen:C1301509|Human Phenotype Ontology:HP:0002376, Human Phenotype Ontology:HP:0002471, Human Phenotype Ontology:HP:0002489, Human Phenotype Ontology:HP:0006797, Human Phenotype Ontology:HP:0006828, Human Phenotype Ontology:HP:0006854, Human Phenotype Ontology:HP:0007037, Human Phenotype Ontology:HP:0007242, Human Phenotype Ontology:HP:0007247, MedGen:C1836830|Human Phenotype Ontology:HP:0002579, MedGen:C1836923|Human Phenotype Ontology:HP:0000754, Human Phenotype Ontology:HP:0001255, Human Phenotype Ontology:HP:0001263, Human Phenotype Ontology:HP:0001277, Human Phenotype Ontology:HP:0001292, Human Phenotype Ontology:HP:0002433, Human Phenotype Ontology:HP:0002473, Human Phenotype Ontology:HP:0002532, Human Phenotype Ontology:HP:0006793, Human Phenotype Ontology:HP:0006867, Human Phenotype Ontology:HP:0006885, Human Phenotype Ontology:HP:0006935, Human Phenotype Ontology:HP:0007005, Human Phenotype Ontology:HP:0007094, Human Phenotype Ontology:HP:0007106, Human Phenotype Ontology:HP:0007174, Human Phenotype Ontology:HP:0007224, Human Phenotype Ontology:HP:0007228, Human Phenotype Ontology:HP:0007342, Human Phenotype Ontology:HP:0025356, MedGen:C0557874|MedGen:C3661900|MONDO:MONDO:0018998, MeSH:D057130, MedGen:C0339527, OMIM:PS204000, Orphanet:65|MONDO:MONDO:0012056, MedGen:C1837873, OMIM:608553, Orphanet:65
ClinVar preferred disease name Retinal dystrophy|Diarrhea|Nystagmus|Severely reduced visual acuity|Developmental regression|Gastrointestinal dysmotility|Global developmental delay|not provided|Leber congenital amaurosis|Leber congenital amaurosis 9
HGVS variant names NC 000001.10:g.10042688G>A
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Pathogenic
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Variant clinical sources reported ClinGen:CA342906|OMIM:608700.0002|UniProtKB:Q9HAN9#VAR 068882
Gene symbol:Gene id. NMNAT1:64802
Molecular consequence SO:0001583|missense variant
Allele origin
dbSNP ID 150726175
For included Variant: Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN Human Phenotype Ontology:HP:0000548, MONDO:MONDO:0015993, MedGen:C4085590, OMIM:PS120970, Orphanet:1872
For included Variant : ClinVar preferred disease name for the concept specified by disease identifiers in CLNDISDB Cone/cone-rod dystrophy
Clinical significance for a haplotype or genotype that includes this variant. Reported as pairs of VariationID:clinical significance. 438483:Pathogenic
Variant Flags

ClinVar @ MSeqDR as full content XML tree

MSeqDR View Variant at Gbrowse

Mitomap Mitochondrial Variant Phenotype Information:


Ensembl Variant Phenotype Information: