chr16:89919736:C>T Detail (hg38) (MC1R)

Information

Genome

Assembly Position
hg19 chr16:89,986,144-89,986,144 View the variant detail on this assembly version.
hg38 chr16:89,919,736-89,919,736

HGVS

Type Transcript Protein
RefSeq NM_002386.3:c.478C>T NP_002377.4:p.Arg160Trp
Ensemble ENST00000555147.2:c.478C>T ENST00000555147.2:p.Arg160Trp
ENST00000555427.1:c.478C>T ENST00000555427.1:p.Arg160Trp
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 tgv56656365 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
Likely benign criteria provided, single submitter not specified germline Detail
Conflicting interpretations of pathogenicity 2023-03-23 criteria provided, conflicting interpretations not provided germline unknown Detail
Benign Likely benign 2024-02-01 criteria provided, multiple submitters, no conflicts Melanoma, cutaneous malignant, susceptibility to, 5 germline Detail
Likely benign no assertion criteria provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<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
0.284 melanoma MC1R gene variants have previously been associated with red hair and fair skin c... BeFree 11179997 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
0.120 INCREASED ANALGESIA FROM KAPPA-OPIOID RECEPTOR AGONIST, FEMALE-SPECIFIC (disorder) NA CLINVAR Detail
<0.001 pheochromocytoma When expressed in rat pheochromocytoma cell line cells, the R151C, R160W and D29... BeFree 19755124 Detail
0.284 melanoma The MC1R melanoma risk variant p.R160W is associated with Parkinson disease. BeFree 25631192 Detail
0.003 Parkinson disease The MC1R melanoma risk variant p.R160W is associated with Parkinson disease. BeFree 25631192 Detail
<0.001 Pallor The R160W MC1R change has previously been implicated in a red hair/pale skin phe... BeFree 22337906 Detail
0.126 vitiligo C478T, one of the MC1R SNPs studied in 108 fair-skinned vitiligo patients and in... BeFree 18282185 Detail
<0.001 VITILIGO-ASSOCIATED MULTIPLE AUTOIMMUNE DISEASE SUSCEPTIBILITY 1 (finding) C478T, one of the MC1R SNPs studied in 108 fair-skinned vitiligo patients and in... BeFree 18282185 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002386.4(MC1R):c.478C>T (p.Arg160Trp) AND Skin/hair/eye pigmentation 2, red hair/fair skin ClinVar Detail
NM_002386.4(MC1R):c.478C>T (p.Arg160Trp) AND Increased analgesia from kappa-opioid receptor agonist,... ClinVar Detail
NM_002386.4(MC1R):c.478C>T (p.Arg160Trp) AND OCULOCUTANEOUS ALBINISM, TYPE II, MODIFIER OF ClinVar Detail
NM_002386.4(MC1R):c.478C>T (p.Arg160Trp) AND not specified ClinVar Detail
NM_002386.4(MC1R):c.478C>T (p.Arg160Trp) AND not provided ClinVar Detail
NM_002386.4(MC1R):c.478C>T (p.Arg160Trp) AND Melanoma, cutaneous malignant, susceptibility to, 5 ClinVar Detail
NM_002386.4(MC1R):c.478C>T (p.Arg160Trp) AND Malignant tumor of breast ClinVar 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
MC1R gene variants have previously been associated with red hair and fair skin color, moreover skin ... 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
NA DisGeNET Detail
When expressed in rat pheochromocytoma cell line cells, the R151C, R160W and D294H MC1R variants ass... DisGeNET Detail
The MC1R melanoma risk variant p.R160W is associated with Parkinson disease. DisGeNET Detail
The MC1R melanoma risk variant p.R160W is associated with Parkinson disease. DisGeNET Detail
The R160W MC1R change has previously been implicated in a red hair/pale skin phenotype, and MC2R -T1... DisGeNET Detail
C478T, one of the MC1R SNPs studied in 108 fair-skinned vitiligo patients and in 70 fair-skinned hea... DisGeNET Detail
C478T, one of the MC1R SNPs studied in 108 fair-skinned vitiligo patients and in 70 fair-skinned hea... 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
rs1805008 dbSNP
Genome
hg38
Position
chr16:89,919,736-89,919,736
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))
rs1805008
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16754
East Asian Chromosome Counts (ExAC)
8558
East Asian Allele Counts (ExAC)
1
East Asian Heterozygous Counts (ExAC)
1
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
1.1684973124561814E-4
Chromosome Counts in All Race (ExAC)
118548
Allele Counts in All Race (ExAC)
5960
Heterozygous Counts in All Race (ExAC)
5458
Homozygous Counts in All Race (ExAC)
251
Allele Frequency in All Race (ExAC)
0.050274994095218815
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