This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
ClinVar Genomic variation as it relates to human health
NM_001258249.2(UTY):c.3197G>A (p.Arg1066His)
Germline
Classification
Help
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.
(1)
Help
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.
Likely benign
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001258249.2(UTY):c.3197G>A (p.Arg1066His)
Variation ID: 2595555 Accession: VCV002595555.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: Yq11.221 Y: 13323634 (GRCh38) [ NCBI UCSC ] Y: 15435514 (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 Oct 28, 2023 May 1, 2024 Jun 22, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001258249.2:c.3197G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001245178.1:p.Arg1066His missense NM_001258250.1:c.2486G>A NP_001245179.1:p.Arg829His missense NM_001258251.1:c.2954G>A NP_001245180.1:p.Arg985His missense NM_001258252.1:c.3041G>A NP_001245181.1:p.Arg1014His missense NM_001258253.1:c.2954G>A NP_001245182.1:p.Arg985His missense NM_001258254.1:c.2669G>A NP_001245183.1:p.Arg890His missense NM_001258255.1:c.2669G>A NP_001245184.1:p.Arg890His missense NM_001258256.1:c.3041G>A NP_001245185.1:p.Arg1014His missense NM_001258257.1:c.2534G>A NP_001245186.1:p.Arg845His missense NM_001258258.1:c.3062G>A NP_001245187.1:p.Arg1021His missense NM_001258259.1:c.2858G>A NP_001245188.1:p.Arg953His missense NM_001258260.1:c.2996G>A NP_001245189.1:p.Arg999His missense NM_001258261.1:c.3032G>A NP_001245190.1:p.Arg1011His missense NM_001258262.1:c.2825G>A NP_001245191.1:p.Arg942His missense NM_001258263.1:c.2906G>A NP_001245192.1:p.Arg969His missense NM_001258264.1:c.2993G>A NP_001245193.1:p.Arg998His missense NM_001258265.1:c.2657G>A NP_001245194.1:p.Arg886His missense NM_001258266.1:c.3041G>A NP_001245195.1:p.Arg1014His missense NM_001258267.1:c.2906G>A NP_001245196.1:p.Arg969His missense NM_001258268.1:c.2669G>A NP_001245197.1:p.Arg890His missense NM_001258269.1:c.2759G>A NP_001245198.1:p.Arg920His missense NM_001258270.1:c.2534G>A NP_001245199.1:p.Arg845His missense NM_001400170.1:c.3041G>A NP_001387099.1:p.Arg1014His missense NM_001400171.1:c.2996G>A NP_001387100.1:p.Arg999His missense NM_001400173.1:c.2906G>A NP_001387102.1:p.Arg969His missense NM_001400175.1:c.3131G>A NP_001387104.1:p.Arg1044His missense NM_001400177.1:c.3131G>A NP_001387106.1:p.Arg1044His missense NM_001400178.1:c.3041G>A NP_001387107.1:p.Arg1014His missense NM_001400181.1:c.2906G>A NP_001387110.1:p.Arg969His missense NM_001400183.1:c.3197G>A NP_001387112.1:p.Arg1066His missense NM_001400185.1:c.3131G>A NP_001387114.1:p.Arg1044His missense NM_001400187.1:c.3089G>A NP_001387116.1:p.Arg1030His missense NM_001400189.1:c.3044G>A NP_001387118.1:p.Arg1015His missense NM_001400192.1:c.3041G>A NP_001387121.1:p.Arg1014His missense NM_001400195.1:c.2996G>A NP_001387124.1:p.Arg999His missense NM_001400199.1:c.2954G>A NP_001387128.1:p.Arg985His missense NM_001419806.1:c.2954G>A NP_001406735.1:p.Arg985His missense NM_007125.4:c.2906G>A NP_009056.3:p.Arg969His missense NM_182659.1:c.2906G>A NP_872600.1:p.Arg969His missense NM_182660.1:c.2906G>A NP_872601.1:p.Arg969His missense NR_047596.1:n.3138G>A non-coding transcript variant NR_047597.1:n.4017G>A non-coding transcript variant NR_047598.1:n.4147G>A non-coding transcript variant NR_047599.1:n.4034G>A non-coding transcript variant NR_047600.1:n.3835G>A non-coding transcript variant NR_047601.1:n.3511G>A non-coding transcript variant NR_047602.1:n.3876G>A non-coding transcript variant NR_047603.1:n.4034G>A non-coding transcript variant NR_047604.1:n.3004G>A non-coding transcript variant NR_047605.1:n.3090G>A non-coding transcript variant NR_047606.1:n.3274G>A non-coding transcript variant NR_047607.1:n.4257G>A non-coding transcript variant NR_047608.1:n.3225G>A non-coding transcript variant NR_047609.1:n.3669G>A non-coding transcript variant NR_047610.1:n.3138G>A non-coding transcript variant NR_047611.1:n.3273G>A non-coding transcript variant NR_047612.1:n.3429G>A non-coding transcript variant NR_047613.1:n.3379G>A non-coding transcript variant NR_047614.1:n.3342G>A non-coding transcript variant NR_047615.1:n.3196G>A non-coding transcript variant NR_047616.1:n.3252G>A non-coding transcript variant NR_047617.1:n.3278G>A non-coding transcript variant NR_047618.1:n.3920G>A non-coding transcript variant NR_047619.1:n.3196G>A non-coding transcript variant NR_047620.1:n.3273G>A non-coding transcript variant NR_047621.1:n.3378G>A non-coding transcript variant NR_047622.1:n.3330G>A non-coding transcript variant NR_047623.1:n.3273G>A non-coding transcript variant NR_047624.1:n.4131G>A non-coding transcript variant NR_047625.1:n.3011G>A non-coding transcript variant NR_047626.1:n.3138G>A non-coding transcript variant NR_047627.1:n.3341G>A non-coding transcript variant NR_047628.1:n.3186G>A non-coding transcript variant NR_047629.1:n.3138G>A non-coding transcript variant NR_047630.1:n.3138G>A non-coding transcript variant NR_047631.1:n.3138G>A non-coding transcript variant NR_047632.1:n.3619G>A non-coding transcript variant NR_047633.1:n.3187G>A non-coding transcript variant NR_047634.1:n.3137G>A non-coding transcript variant NR_047635.1:n.3906G>A non-coding transcript variant NR_047636.1:n.3276G>A non-coding transcript variant NR_047637.1:n.3969G>A non-coding transcript variant NR_047638.1:n.3977G>A non-coding transcript variant NR_047639.1:n.3044G>A non-coding transcript variant NR_047640.1:n.3122G>A non-coding transcript variant NR_047641.1:n.3911G>A non-coding transcript variant NR_047642.1:n.3911G>A non-coding transcript variant NR_047643.1:n.3511G>A non-coding transcript variant NR_047644.1:n.4104G>A non-coding transcript variant NR_047645.1:n.4117G>A non-coding transcript variant NR_047646.1:n.3784G>A non-coding transcript variant NR_047647.1:n.3868G>A non-coding transcript variant NR_174404.1:n.2657G>A non-coding transcript variant NR_174405.1:n.3274G>A non-coding transcript variant NC_000024.10:g.13323634C>T NC_000024.9:g.15435514C>T - Protein change
- R829H, R845H, R969H, R1011H, R1030H, R1066H, R890H, R953H, R999H, R1014H, R1015H, R920H, R942H, R1021H, R1044H, R886H, R985H, R998H
- Other names
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- Canonical SPDI
- NC_000024.10:13323633:C:T
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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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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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- 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 | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
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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| UTY | - | - |
GRCh38 GRCh37 |
3 | 68 | |
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. |
|---|---|---|---|---|
| Likely benign (1) |
criteria provided, single submitter
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Jun 22, 2023 | RCV004342439.1 |
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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Likely benign
(Jun 22, 2023)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV004068253.2
First in ClinVar: Oct 28, 2023 Last updated: May 01, 2024 |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more)
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
|
Comment:
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. |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
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.