Variant
GAMT Y49Ifs*65
NM_000156.6(GAMT):c.145del (p.Tyr49IlefsTer65)
- p.Tyr49IlefsTer65
- p.Y49Ifs*65
- rs1384688313
- ClinVar classification
- Pathogenic
- Review status
- 3 stars out of 4reviewed by expert panel
- Last evaluated
- 14 September 2023
- Expert panel
- ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel, ClinGen
Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.16-c6eea6bfFacts last changed 16 October 2026
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
Summary
Y49Ifs*65 is a frameshift variant in GAMT: it adds or removes DNA letters in a way that shifts how the rest of the gene's code is read. ClinVar classifies it as pathogenic for guanidinoacetate methyltransferase deficiency (reviewed by expert panel).
ClinVar classifications
| Condition | Classification | Review status | Submissions | Last evaluated |
|---|---|---|---|---|
| guanidinoacetate methyltransferase deficiencyClinVar VCV000695019 (opens in a new tab) | Pathogenic | 3 stars out of 4reviewed by expert panel | 1 submission | 14 September 2023 |
Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed.
Where it lies in GAMT
Y49Ifs*65 lies in exon 1 of the 6 in GAMT's MANE Select transcript, NM_000156.6.
Molecular details
| Gene | GAMT |
|---|---|
| Transcript | NM_000156.6MANE Select |
| Coding DNA change (HGVS c.) | c.145del |
| Protein change (HGVS p.) | p.Tyr49IlefsTer65p.Y49Ifs*65 |
| Predicted consequence | Frameshiftframeshift_variant (opens in a new tab)frameshift_truncation (opens in a new tab) |
| Predicted impact | High |
| Position (GRCh38) | chr19:1401331 TA>T |
| Position (GRCh37) | chr19:1401330 TA>T |
| dbSNP ID | rs1384688313 (opens in a new tab) |
| ClinVar Variation ID | VCV000695019 (opens in a new tab) |
| ClinVar Allele ID | 683148 |
| ClinGen Allele Registry ID | CA631301060 (opens in a new tab) |
| ClinVar name | NM_000156.6(GAMT):c.145del (p.Tyr49fs) |
GAMT Y49Ifs*65 in other databases
Reports that look at this variant (1)
These Genome Test condition reports include Y49Ifs*65 among the variants they look at.
| Report | Conditions | Inheritance |
|---|---|---|
| Cerebral Creatine Deficiency Syndromes | Cerebral Creatine Deficiency Syndrome |
Other variants in GAMT
- A22Gfs*63Pathogenic3 stars out of 4
- A54PLikely pathogenic3 stars out of 4
- A74PLikely pathogenic3 stars out of 4
- A75VPathogenic3 stars out of 4
- A156DLikely pathogenic3 stars out of 4
- c.1A>GLikely pathogenic3 stars out of 4
- c.114C>TLikely pathogenic3 stars out of 4
- c.158_181+7delPathogenic3 stars out of 4
- c.327+43G>ALikely pathogenic3 stars out of 4
- c.327G>APathogenic3 stars out of 4
Limitations
This page describes publicly available information about a genetic variant. It is not a diagnosis, and it says nothing about whether you or anyone else carries this variant.
Classifications come from ClinVar and change as new evidence is reviewed. A classification here may differ from the one in ClinVar today, or from the one a laboratory reports.
Whole genome sequencing with short reads can miss or miscall some variants, particularly in repeated or highly similar stretches of DNA and in large insertions, deletions or rearrangements.
If you have questions about a variant in your own results or in your family, talk to a genetic counsellor or your doctor.
Sources & credits
- Classifications from ClinVar (release 2026-10-12), National Center for Biotechnology Information.
- Condition terms from the Mondo Disease Ontology (release 2026-10-06), used under CC BY 4.0.
- Gene symbols and names from the HUGO Gene Nomenclature Committee (release 2026-10-16).
- Allele identifiers from the ClinGen Allele Registry (release 2026-10-16-c4908f54).
- Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information.
- Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-16).
- Difficult regions from the Genome in a Bottle Consortium (release v3.6).
- Transcripts from MANE (release v1.5), NCBI and EMBL-EBI.
- Predicted consequences from mehari (release 0.11.0), with transcript models from cdot.
- Built from Dante Labs data release 2026.10.16-c6eea6bf of 16 October 2026.
Cite this page
Dante Labs. (16 October 2026). GAMT Y49Ifs*65 (c.145del, rs1384688313) (Version 2026.10.16-c6eea6bf). Retrieved 16 October 2026, from https://dantelabs.com/genes/gamt/variants/y49ifs65
Dante Labs. GAMT Y49Ifs*65 (c.145del, rs1384688313) [Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 [cited 16 October 2026]. Available from: https://dantelabs.com/genes/gamt/variants/y49ifs65
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