Is PTF1A p.Asp34= (c.102C>T) pathogenic?

PTF1A p.Asp34= (c.102C>T) is classified Benign/Likely benign in PTF1A (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-01-13). Rare (popmax 0.747%, eas); Associated with permanent neonatal diabetes mellitus-pancreatic and cerebellar agenesis syndrome.

How common is PTF1A p.Asp34= (c.102C>T) in the general population?

PTF1A p.Asp34= (c.102C>T) is rare (popmax 0.747%, eas) (gnomAD).

PTF1A p.Asp34=

Q: What condition is associated with PTF1A p.Asp34= (c.102C>T)?

PTF1A p.Asp34= (c.102C>T) is associated with permanent neonatal diabetes mellitus-pancreatic and cerebellar agenesis syndrome (ClinVar).

c.102C>T · rs199831799 · VCV299621

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.747%, eas)

Conditions

permanent neonatal diabetes mellitus-pancreatic and cerebellar agenesis syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.76	GERP 0.071, phastCons 1
Overall
CADD	7.724	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.747% East Asian · 322/43,134 alleles

Filtering AF 0.679% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.653%

Overall 0.0217% 347/1,601,800 alleles · rare exomes 309/1,449,592 · genomes 38/152,208 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.747%	134
Remaining individualsnot grpmax-eligible	0.0193%	5,170
Admixed American	0.00677%	14,766
South Asian	0.00445%	22,486
European (non-Finnish)	0.000426%	234,904

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PTF1A
Protein: p.Asp34=
Coding: c.102C>T
MANE Select: NM_178161
dbSNP: rs199831799
Type: single nucleotide variant
Location: chr10:23192632 (GRCh38)
Gene constraint: LOEUF 1.878 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.81

Full PTF1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

permanent neonatal diabetes mellitus-pancreatic and cerebellar agenesis syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PTF1A p.Pro191Thr Pathogenic/Likely pathogenic ★★ same condition
PTF1A p.Ala149Val Uncertain significance ★★ ⚠ same condition
PTF1A p.Ala3Val Uncertain significance ★★ ⚠ same condition
PTF1A p.Arg206Leu Uncertain significance ★★ ⚠ same condition
PTF1A p.Cys121Tyr Uncertain significance ★★ ⚠ same condition
PTF1A p.Gly88Asp Uncertain significance ★★ ⚠ same condition
PTF1A p.Leu89Ile Uncertain significance ★★ ⚠ same condition
PTF1A c.*15G>A Benign/Likely benign ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ptf1a-p-asp34 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown