ClinVar Genomic variation as it relates to human health
NM_000372.5(TYR):c.230G>A (p.Arg77Gln)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000372.5(TYR):c.230G>A (p.Arg77Gln)
Variation ID: 3776 Accession: VCV000003776.45
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 11q14.3 11: 89178183 (GRCh38) [ NCBI UCSC ] 11: 88911351 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Nov 17, 2024 Sep 19, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000372.5:c.230G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000363.1:p.Arg77Gln missense NC_000011.10:g.89178183G>A NC_000011.9:g.88911351G>A NG_008748.1:g.5312G>A P14679:p.Arg77Gln - Protein change
- R77Q
- Other names
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R59Q
- Canonical SPDI
- NC_000011.10:89178182:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00040 (A)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD) 0.00006
Trans-Omics for Precision Medicine (TOPMed) 0.00006
The Genome Aggregation Database (gnomAD), exomes 0.00008
Exome Aggregation Consortium (ExAC) 0.00010
1000 Genomes Project 30x 0.00031
1000 Genomes Project 0.00040
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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TYR | - | - |
GRCh38 GRCh37 |
689 | 710 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (7) |
criteria provided, multiple submitters, no conflicts
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Jul 22, 2021 | RCV000003975.14 | |
Pathogenic (6) |
criteria provided, multiple submitters, no conflicts
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Jan 4, 2024 | RCV000085934.33 | |
Pathogenic (1) |
no assertion criteria provided
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Jan 29, 2019 | RCV000984954.3 | |
See cases
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Pathogenic (1) |
criteria provided, single submitter
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Dec 21, 2022 | RCV003156054.2 |
Pathogenic (1) |
criteria provided, single submitter
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May 3, 2022 | RCV002476921.2 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Mar 14, 2024 | RCV003466800.5 | |
TYR-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Jul 26, 2024 | RCV004532282.2 |
Pathogenic (1) |
criteria provided, single submitter
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Sep 19, 2024 | RCV004782006.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Mar 16, 2015)
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criteria provided, single submitter
Method: clinical testing
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Albinism, oculocutaneous, type IA
Affected status: yes
Allele origin:
germline
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Genetic Services Laboratory, University of Chicago
Accession: SCV000249336.1
First in ClinVar: Oct 05, 2015 Last updated: Oct 05, 2015 |
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Pathogenic
(Jul 12, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000855376.1
First in ClinVar: Feb 20, 2014 Last updated: Feb 20, 2014 |
Number of individuals with the variant: 1
Sex: mixed
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Pathogenic
(Jul 22, 2021)
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criteria provided, single submitter
Method: clinical testing
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Tyrosinase-negative oculocutaneous albinism
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV001821923.1
First in ClinVar: Sep 08, 2021 Last updated: Sep 08, 2021 |
Sex: mixed
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Pathogenic
(May 03, 2022)
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criteria provided, single submitter
Method: clinical testing
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Tyrosinase-negative oculocutaneous albinism
SKIN/HAIR/EYE PIGMENTATION 3, LIGHT/DARK SKIN Oculocutaneous albinism type 1B
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002785299.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Jan 11, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV003823791.2
First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024 |
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Pathogenic
(Jan 04, 2024)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV002139732.3
First in ClinVar: Mar 28, 2022 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 77 of the TYR protein (p.Arg77Gln). … (more)
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 77 of the TYR protein (p.Arg77Gln). This variant is present in population databases (rs61753185, gnomAD 0.01%). This missense change has been observed in individuals with oculocutaneous albinism (PMID: 21985232, 31077556). ClinVar contains an entry for this variant (Variation ID: 3776). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt TYR protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects TYR function (PMID: 21985232). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Mar 14, 2024)
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criteria provided, single submitter
Method: research
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SKIN/HAIR/EYE PIGMENTATION 3, LIGHT/DARK SKIN
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV004801134.2
First in ClinVar: Mar 16, 2024 Last updated: Apr 06, 2024 |
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Pathogenic
(Feb 09, 2017)
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criteria provided, single submitter
Method: clinical testing
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Tyrosinase-negative oculocutaneous albinism
Affected status: yes
Allele origin:
germline
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Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota
Accession: SCV000890897.1
First in ClinVar: Mar 19, 2019 Last updated: Mar 19, 2019 |
Number of individuals with the variant: 1
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Tyrosinase-negative oculocutaneous albinism
Affected status: yes
Allele origin:
germline
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Pathology and Clinical Laboratory Medicine, King Fahad Medical City
Accession: SCV000996277.1
First in ClinVar: Oct 19, 2019 Last updated: Oct 19, 2019 |
Number of individuals with the variant: 3
Ethnicity/Population group: Arab
Geographic origin: Middle East
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Pathogenic
(Jan 22, 2020)
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criteria provided, single submitter
Method: clinical testing
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Tyrosinase-negative oculocutaneous albinism
Affected status: yes
Allele origin:
unknown
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Baylor Genetics
Accession: SCV001524703.1
First in ClinVar: Mar 22, 2021 Last updated: Mar 22, 2021 |
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
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Pathogenic
(May 26, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000779692.3
First in ClinVar: Feb 20, 2014 Last updated: Mar 04, 2023 |
Comment:
Published functional studies demonstrate a damaging effect: abnormal protein folding and no in vitro enzyme activity (Dolinksa et al., 2017); This variant is associated with … (more)
Published functional studies demonstrate a damaging effect: abnormal protein folding and no in vitro enzyme activity (Dolinksa et al., 2017); This variant is associated with the following publications: (PMID: 23324268, 2113511, 1642278, 32552793, 10929771, 32427313, 21985232, 34487524, 27775880, 31077556, 28976636) (less)
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Pathogenic
(Dec 21, 2022)
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criteria provided, single submitter
Method: clinical testing
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See cases
Affected status: yes
Allele origin:
unknown
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Center for Personalized Medicine, Children's Hospital Los Angeles
Accession: SCV003845333.1
First in ClinVar: Apr 01, 2023 Last updated: Apr 01, 2023 |
Clinical Features:
Abnormality of hair pigmentation (present) , Albinism (present) , Microcytic anemia (present) , Normochromic microcytic anemia (present) , Ocular albinism (present) , Patent foramen ovale … (more)
Abnormality of hair pigmentation (present) , Albinism (present) , Microcytic anemia (present) , Normochromic microcytic anemia (present) , Ocular albinism (present) , Patent foramen ovale (present) , Pulmonary arterial hypertension (present) , Recurrent Klebsiella infections (present) , Thrombocytopenia (present) (less)
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Pathogenic
(Mar 11, 2024)
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criteria provided, single submitter
Method: clinical testing
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SKIN/HAIR/EYE PIGMENTATION 3, LIGHT/DARK SKIN
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004207559.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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Pathogenic
(Mar 01, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV002497161.18
First in ClinVar: Apr 08, 2022 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 2
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Pathogenic
(Sep 19, 2024)
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criteria provided, single submitter
Method: clinical testing
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Oculocutaneous albinism
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV005395371.1
First in ClinVar: Nov 17, 2024 Last updated: Nov 17, 2024 |
Comment:
Variant summary: TYR c.230G>A (p.Arg77Gln) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging … (more)
Variant summary: TYR c.230G>A (p.Arg77Gln) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8.4e-05 in 251030 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in TYR causing Oculocutaneous Albinism (8.4e-05 vs 0.0056), allowing no conclusion about variant significance. c.230G>A has been reported in the literature in multiple individuals affected with Oculocutaneous Albinism (example, Shah_2015,Takeda_1989). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in diminished catalytical activity in mouse amelanotic melanoma cells (Takeda_1989). The following publications have been ascertained in the context of this evaluation (PMID: 25703744, 2120217). ClinVar contains an entry for this variant (Variation ID: 3776). Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(Jul 15, 1992)
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no assertion criteria provided
Method: literature only
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ALBINISM, OCULOCUTANEOUS, TYPE IA
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000024140.1
First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013 |
Comment on evidence:
By enzymatic DNA amplification and direct DNA sequencing, Kikuchi et al. (1990) demonstrated a G-to-A change in nucleotide 309. This was thought to result in … (more)
By enzymatic DNA amplification and direct DNA sequencing, Kikuchi et al. (1990) demonstrated a G-to-A change in nucleotide 309. This was thought to result in a change of arginine-77 to glutamine. Also see Tripathi et al. (1992). (less)
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Pathogenic
(Jul 26, 2024)
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no assertion criteria provided
Method: clinical testing
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TYR-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004114465.2
First in ClinVar: Nov 20, 2023 Last updated: Oct 08, 2024 |
Comment:
The TYR c.230G>A variant is predicted to result in the amino acid substitution p.Arg77Gln. This variant has been reported in the homozygous and compound heterozygous … (more)
The TYR c.230G>A variant is predicted to result in the amino acid substitution p.Arg77Gln. This variant has been reported in the homozygous and compound heterozygous states in individuals with oculocutaneous albinism (see for examples Kikuchi et al. 1990. PubMed ID: 2113511; Kono et al. 2012. PubMed ID: 21985232; Marti et al. 2018. PubMed ID: 28976636). Functional studies support the pathogenicity of this variant (Dolinska et al. 2017. PubMed ID: 27775880; Kono et al. 2012. PubMed ID: 219852320). This variant is reported in 0.012% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant has been classified as pathogenic by multiple independent submitters to the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/3776/). Given all the evidence, we interpret this variant as pathogenic. (less)
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Pathogenic
(Jan 29, 2019)
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no assertion criteria provided
Method: clinical testing
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Oculocutaneous albinism type 1B
Affected status: yes
Allele origin:
germline
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Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City
Accession: SCV001132868.1
First in ClinVar: Jan 06, 2020 Last updated: Jan 06, 2020 |
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Pathogenic
(Jan 29, 2019)
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no assertion criteria provided
Method: clinical testing
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Tyrosinase-negative oculocutaneous albinism
Affected status: yes
Allele origin:
germline
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Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City
Accession: SCV001132869.1
First in ClinVar: Jan 06, 2020 Last updated: Jan 06, 2020 |
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not provided
(-)
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no classification provided
Method: not provided
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not provided
Affected status: not provided
Allele origin:
unknown
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Retina International
Accession: SCV000118077.1
First in ClinVar: Feb 20, 2014 Last updated: Feb 20, 2014
Comment:
http://phencode.bx.psu.edu/cgi-bin/phencode/phencode?build=hg19&id=RISN_TYR:c.230G>A
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Comprehensive analysis of spectral distribution of a large cohort of Chinese patients with non-syndromic oculocutaneous albinism facilitates genetic diagnosis. | Zhong Z | Pigment cell & melanoma research | 2019 | PMID: 31077556 |
Mutational spectrum of the TYR and SLC45A2 genes in Pakistani families with oculocutaneous albinism, and potential founder effect of missense substitution (p.Arg77Gln) of tyrosinase. | Shah SA | Clinical and experimental dermatology | 2015 | PMID: 25703744 |
Mutation spectrum of the TYR and SLC45A2 genes in patients with oculocutaneous albinism. | Ko JM | Molecular medicine reports | 2012 | PMID: 22294196 |
Molecular analysis of Korean patients with oculocutaneous albinism. | Park SH | Japanese journal of ophthalmology | 2012 | PMID: 22042571 |
Genotype analysis in a patient with oculocutaneous albinism 1 minimal pigment type. | Kono M | The British journal of dermatology | 2012 | PMID: 21985232 |
Tyrosinase gene mutations in type I (tyrosinase-deficient) oculocutaneous albinism define two clusters of missense substitutions. | Tripathi RK | American journal of medical genetics | 1992 | PMID: 1642278 |
Molecular basis of tyrosinase-negative oculocutaneous albinism. A single base mutation in the tyrosinase gene causing arginine to glutamine substitution at position 59. | Takeda A | The Journal of biological chemistry | 1990 | PMID: 2120217 |
Detection of point mutation in the tyrosinase gene of a Japanese albino patient by a direct sequencing of amplified DNA. | Kikuchi H | Human genetics | 1990 | PMID: 2113511 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=TYR | - | - | - | - |
Text-mined citations for rs61753185 ...
HelpRecord last updated Nov 25, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.