chr16:89919709:C>T Detail (hg38) (MC1R)

Information

Genome

Assembly Position
hg19 chr16:89,986,117-89,986,117 View the variant detail on this assembly version.
hg38 chr16:89,919,709-89,919,709

HGVS

Type Transcript Protein
RefSeq NM_002386.3:c.451C>T NP_002377.4:p.Arg151Cys
Ensemble ENST00000555147.2:c.451C>T ENST00000555147.2:p.Arg151Cys
ENST00000555427.1:c.451C>T ENST00000555427.1:p.Arg151Cys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 155555 OMIM
HGNC 6929 HGNC
Ensembl ENSG00000258839 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv56656347 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
association 2015-05-01 no assertion criteria provided Skin/hair/eye pigmentation 2, red hair/fair skin germline Detail
Affects 2015-05-01 no assertion criteria provided Increased analgesia from kappa-opioid receptor agonist, female-specific germline Detail
risk factor 2015-05-01 no assertion criteria provided OCULOCUTANEOUS ALBINISM, TYPE II, MODIFIER OF germline Detail
Benign criteria provided, single submitter not specified germline Detail
Conflicting interpretations of pathogenicity 2022-07-21 criteria provided, conflicting interpretations not provided germline unknown Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Melanoma, cutaneous malignant, susceptibility to, 5 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2 (disorder) Sequence analysis demonstrated a known deleterious mutation in CDKN2A (G-34T) an... BeFree 18025365 Detail
0.005 SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2 (disorder) Sequence analysis demonstrated a known deleterious mutation in CDKN2A (G-34T) an... BeFree 18025365 Detail
<0.001 melanoma We aim to examine the influence of the MC1R variants (RHC: D84E, R151C, R160W; N... BeFree 24170137 Detail
0.003 Erythema Persons carrying MC1R homozygote variant alleles at R151C, R160W, D294H and D84E... BeFree 20129839 Detail
<0.001 pheochromocytoma When expressed in rat pheochromocytoma cell line cells, the R151C, R160W and D29... BeFree 19755124 Detail
<0.001 Experimental Organism Basal Cell Carcinoma A non-synonymous SNP in the MC1R gene (rs1805007 encoding Arg151Cys substitution... BeFree 21700618 Detail
0.284 melanoma MC1R gene variants have previously been associated with red hair and fair skin c... BeFree 11179997 Detail
0.122 Sunburn Genome-wide association studies identify several new loci associated with pigmen... GWASCAT 23548203 Detail
0.125 Freckles Genetic determinants of hair, eye and skin pigmentation in Europeans. GWASCAT 17952075 Detail
0.126 skin carcinoma Genome-wide association studies identify several new loci associated with pigmen... GWASCAT 23548203 Detail
0.005 SKIN/HAIR/EYE PIGMENTATION, VARIATION IN, 2 (disorder) Measures included past sun exposure by calendar and questionnaire, spectrophotom... BeFree 18711112 Detail
0.014 Malignant neoplasm of skin We studied the desensitization and internalization of three variant MC1R forms a... BeFree 17130136 Detail
<0.001 pheochromocytoma When expressed in rat pheochromocytoma cell line cells, the R151C, R160W and D29... BeFree 19755124 Detail
0.005 Experimental Organism Basal Cell Carcinoma A non-synonymous SNP in the MC1R gene (rs1805007 encoding Arg151Cys substitution... BeFree 21700618 Detail
0.005 Experimental Organism Basal Cell Carcinoma The p.(Arg151Cys) variant in MC1R (rs1805007) was associated with an earlier med... BeFree 25159867 Detail
0.120 INCREASED ANALGESIA FROM KAPPA-OPIOID RECEPTOR AGONIST, FEMALE-SPECIFIC (disorder) NA CLINVAR Detail
0.284 melanoma Furthermore, we observed that a carrier of the founder CDKN2A [p.Leu113Leu;p.Pro... BeFree 17492760 Detail
<0.001 pheochromocytoma When expressed in rat pheochromocytoma cell line cells, the R151C, R160W and D29... BeFree 19755124 Detail
0.257 basal cell carcinoma [A non-synonymous SNP in the MC1R gene (rs1805007 encoding Arg151Cys substitutio... GAD 21700618 Detail
0.257 basal cell carcinoma A non-synonymous SNP in the MC1R gene (rs1805007 encoding Arg151Cys substitution... GWASCAT 21700618 Detail
0.284 melanoma Two MC1R germline variants, Arg151Cys and Asp294His, were significantly associat... BeFree 19799798 Detail
0.125 Freckles [Genetic determinants of hair, eye and skin pigmentation in Europeans.] GAD 17952075 Detail
0.284 melanoma Furthermore, a non-significant tendency towards an association between melanoma ... BeFree 22621339 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002386.4(MC1R):c.451C>T (p.Arg151Cys) AND Skin/hair/eye pigmentation 2, red hair/fair skin ClinVar Detail
NM_002386.4(MC1R):c.451C>T (p.Arg151Cys) AND Increased analgesia from kappa-opioid receptor agonist,... ClinVar Detail
NM_002386.4(MC1R):c.451C>T (p.Arg151Cys) AND OCULOCUTANEOUS ALBINISM, TYPE II, MODIFIER OF ClinVar Detail
NM_002386.4(MC1R):c.451C>T (p.Arg151Cys) AND not specified ClinVar Detail
NM_002386.4(MC1R):c.451C>T (p.Arg151Cys) AND not provided ClinVar Detail
NM_002386.4(MC1R):c.451C>T (p.Arg151Cys) AND Melanoma, cutaneous malignant, susceptibility to, 5 ClinVar Detail
Sequence analysis demonstrated a known deleterious mutation in CDKN2A (G-34T) and homozygosity for a... DisGeNET Detail
Sequence analysis demonstrated a known deleterious mutation in CDKN2A (G-34T) and homozygosity for a... DisGeNET Detail
We aim to examine the influence of the MC1R variants (RHC: D84E, R151C, R160W; NRHC: V60L, R163Q and... DisGeNET Detail
Persons carrying MC1R homozygote variant alleles at R151C, R160W, D294H and D84E were more likely to... DisGeNET Detail
When expressed in rat pheochromocytoma cell line cells, the R151C, R160W and D294H MC1R variants ass... DisGeNET Detail
A non-synonymous SNP in the MC1R gene (rs1805007 encoding Arg151Cys substitution), a previously well... DisGeNET Detail
MC1R gene variants have previously been associated with red hair and fair skin color, moreover skin ... DisGeNET Detail
Genome-wide association studies identify several new loci associated with pigmentation traits and sk... DisGeNET Detail
Genetic determinants of hair, eye and skin pigmentation in Europeans. DisGeNET Detail
Genome-wide association studies identify several new loci associated with pigmentation traits and sk... DisGeNET Detail
Measures included past sun exposure by calendar and questionnaire, spectrophotometric skin type, and... DisGeNET Detail
We studied the desensitization and internalization of three variant MC1R forms associated with red h... DisGeNET Detail
When expressed in rat pheochromocytoma cell line cells, the R151C, R160W and D294H MC1R variants ass... DisGeNET Detail
A non-synonymous SNP in the MC1R gene (rs1805007 encoding Arg151Cys substitution), a previously well... DisGeNET Detail
The p.(Arg151Cys) variant in MC1R (rs1805007) was associated with an earlier median age of onset of ... DisGeNET Detail
NA DisGeNET Detail
Furthermore, we observed that a carrier of the founder CDKN2A [p.Leu113Leu;p.Pro114Ser] mutation as ... DisGeNET Detail
When expressed in rat pheochromocytoma cell line cells, the R151C, R160W and D294H MC1R variants ass... DisGeNET Detail
[A non-synonymous SNP in the MC1R gene (rs1805007 encoding Arg151Cys substitution), a previously wel... DisGeNET Detail
A non-synonymous SNP in the MC1R gene (rs1805007 encoding Arg151Cys substitution), a previously well... DisGeNET Detail
Two MC1R germline variants, Arg151Cys and Asp294His, were significantly associated with melanoma in ... DisGeNET Detail
[Genetic determinants of hair, eye and skin pigmentation in Europeans.] DisGeNET Detail
Furthermore, a non-significant tendency towards an association between melanoma risk and MC1R varian... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1805007 dbSNP
Genome
hg38
Position
chr16:89,919,709-89,919,709
Variant Type
snv
Reference Allele
C
Alternative Allele
T
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs1805007
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0009
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
15
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16754
East Asian Chromosome Counts (ExAC)
8566
East Asian Allele Counts (ExAC)
8
East Asian Heterozygous Counts (ExAC)
8
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
9.339248190520663E-4
Chromosome Counts in All Race (ExAC)
119912
Allele Counts in All Race (ExAC)
5382
Heterozygous Counts in All Race (ExAC)
4978
Homozygous Counts in All Race (ExAC)
202
Allele Frequency in All Race (ExAC)
0.044882914137033825
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