Is DTD2 p.Leu13Phe (c.37C>T) pathogenic?

DTD2 p.Leu13Phe (c.37C>T) is classified Uncertain significance in DTD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-08). AlphaMissense: ambiguous (0.5629); Absent from gnomAD v4.1.

How common is DTD2 p.Leu13Phe (c.37C>T) in the general population?

DTD2 p.Leu13Phe (c.37C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DTD2 p.Leu13Phe (c.37C>T)?

AlphaMissense predicts ambiguous (score 0.5629) — an in-silico prediction, not a clinical call.

DTD2 p.Leu13Phe

c.37C>T · VCV3273943

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5629 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,587,986)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.5629	ambiguous
REVEL	0.277	benign-leaning
SaProt	LLR -9.35	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.6	GERP -0.24, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 9,261 bp · p 0.029 · regional, not allelic
Overall
CADD	27.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,587,986). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DTD2
Protein: p.Leu13Phe
Coding: c.37C>T
MANE Select: NM_080664
Type: single nucleotide variant
Location: chr14:31457357 (GRCh38)
Gene constraint: LOEUF 1.429 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.31

Full DTD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DTD2 p.Ala12Glu Uncertain significance ★ ⚠ same type
DTD2 p.Arg102Gly Uncertain significance ★ ⚠ same type
DTD2 p.Gln121Pro Uncertain significance ★ ⚠ same type
DTD2 p.Gly149Arg Uncertain significance ★ ⚠ same type
DTD2 p.Ile166Thr Uncertain significance ★ ⚠ same type
DTD2 p.Met104Arg Uncertain significance ★ ⚠ same type
DTD2 p.Met60Thr Uncertain significance ★ ⚠ same type
DTD2 p.Phe168Ile Uncertain significance ★ ⚠ same type

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/dtd2-p-leu13phe (accessed [today's date]).

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