Is DTHD1 p.Asp656Glu (c.1968T>G) pathogenic?

DTHD1 p.Asp656Glu (c.1968T>G) is classified Uncertain significance in DTHD1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-09-25). AlphaMissense: likely benign (0.1274); Very rare (popmax 0.000436%, nfe).

How common is DTHD1 p.Asp656Glu (c.1968T>G) in the general population?

DTHD1 p.Asp656Glu (c.1968T>G) is very rare (popmax 0.000436%, nfe) (gnomAD).

What do computational predictors say about DTHD1 p.Asp656Glu (c.1968T>G)?

AlphaMissense predicts likely benign (score 0.1274) — an in-silico prediction, not a clinical call.

DTHD1 p.Asp656Glu

c.1968T>G · rs1379530079 · VCV1382156

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1274 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000436%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1274	likely benign
REVEL	0.092	moderately benign-leaning
SaProt	LLR -6.33	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.38	phastCons 0.013
Regional constraint	o/e 0.99	unconstrained · MANE · 62 kb · p 0.66 · regional, not allelic
Overall
CADD	0.091	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM D531E vs ClinVar D656E) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000436% European (non-Finnish) · 5/1,147,020 alleles

Filtering AF 0.000128% ClinGen BA1/BS1 input FAF95, joint · FAF99 9.3e-05%

Overall 0.000322% 5/1,551,808 alleles · very rare exomes 5/1,399,482 · genomes 0/152,326 · joint denominator

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: DTHD1
Protein: p.Asp656Glu
Coding: c.1968T>G
MANE Select: NM_001170700
dbSNP: rs1379530079
Type: single nucleotide variant
Location: chr4:36308366 (GRCh38)
Gene constraint: LOEUF 1.034 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.99

Full DTHD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DTHD1 p.Asp656Ala Uncertain significance ★ ⚠ same residue
DTHD1 c.1218+1G>A Uncertain significance ★★ same type
DTHD1 c.1219-2A>G Uncertain significance ★★ same type
DTHD1 p.Ala552Ser Uncertain significance ★★ ⚠ same type
DTHD1 p.Ala811Asp Uncertain significance ★★ ⚠ same type
DTHD1 p.Arg326Gln Uncertain significance ★★ ⚠ same type
DTHD1 p.Arg371Cys Uncertain significance ★★ ⚠ same type
DTHD1 p.Arg447Gln 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/dthd1-p-asp656glu (accessed [today's date]).

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