Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Link to SEPIO compliant JSON-LD document

Variant: NM_001306179.2:c.327-1G>T

CA386958695

Gene: HNF1A

Condition: monogenic diabetes

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: e4307025-d837-4d3d-9424-c6f68a1beef2

HGVS expressions

NM_001306179.2:c.327-1G>T

NC_000012.12:g.120988832G>T

CM000674.2:g.120988832G>T

NC_000012.11:g.121426635G>T

CM000674.1:g.121426635G>T

NC_000012.10:g.119911018G>T

NG_011731.2:g.15087G>T

ENST00000257555.11:c.327-1G>T

ENST00000257555.10:c.327-1G>T

ENST00000400024.6:c.327-1G>T

ENST00000402929.5:n.462-1G>T

ENST00000535955.5:n.43-8659G>T

ENST00000538626.2:n.191-8659G>T

ENST00000538646.5:c.327-1G>T

ENST00000540108.1:c.327-4688G>T

ENST00000541395.5:c.327-1G>T

ENST00000541924.5:c.327-1G>T

ENST00000543427.5:c.327-1G>T

ENST00000544413.2:c.327-1G>T

ENST00000544574.5:c.73-7785G>T

ENST00000560968.5:n.470-1G>T

ENST00000615446.4:c.-257-7430G>T

ENST00000617366.4:c.327-1G>T

NM_000545.5:c.327-1G>T

NM_000545.6:c.327-1G>T

NM_001306179.1:c.327-1G>T

NM_000545.8:c.327-1G>T

Pathogenic

PS1_Supporting PM2_Supporting PVS1

Evidence Links 0

Expert Panel

Monogenic Diabetes VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Monogenic Diabetes VCEP

The c.327-1G>T variant in the HNF1 homeobox A gene, HNF1A, is a single nucleotide variant within intron 1 of NM_000545.8. This variant is absent from gnomAD 2.1.1 (PM2_Supporting). This variant is predicted to cause skipping of biologically-relevant exon 1 of 10, resulting in a frameshift, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID: 23348805). The c.327-1G>A variant at the same canonical nucleotide has been classified as pathogenic for monogenic diabetes by the ClinGen MDEP, and c.327-1G>T has a similar predicted impact on splice acceptor loss by Splice AI (0.99) as c.327-1G>A (1.00) (PS1_Supporting). In summary, this variant meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.1, approved 9/30/2021): PVS1, PM2_Supporting, PS1_Supporting.

PS1_Supporting

The c.327-1G>A variant at the same canonical nucleotide has been classified as pathogenic for monogenic diabetes by the ClinGen MDEP, and c.327-1G>T has a similar predicted impact on splice acceptor loss by Splice AI (0.99) as c.327-G>A (1.00).

PM2_Supporting

Absent from gnomAD.

PVS1

This variant is predicted to cause skipping of biologically-relevant exon 1 of 10, resulting in a frameshift, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism.

Approved on: 2022-04-18

Published on: 2022-04-18

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