Is DPT p.Val59Met (c.175G>A) pathogenic?

DPT p.Val59Met (c.175G>A) is classified Uncertain significance in DPT (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-02). AlphaMissense: likely benign (0.1887); Ultra-rare (popmax 0.04%, afr).

How common is DPT p.Val59Met (c.175G>A) in the general population?

DPT p.Val59Met (c.175G>A) is ultra-rare (popmax 0.04%, afr) (gnomAD).

What do computational predictors say about DPT p.Val59Met (c.175G>A)?

AlphaMissense predicts likely benign (score 0.1887) — an in-silico prediction, not a clinical call.

DPT p.Val59Met

c.175G>A · rs146462912 · VCV2358798

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1887 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.04%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1887	likely benign
REVEL	0.097	moderately benign-leaning
SaProt	LLR -7.81	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 3.3	GERP 0.023, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 33 kb · p 0.84 · regional, not allelic
Overall
CADD	25.0	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.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.04% African / African-American · 30/75,052 alleles

Filtering AF 0.0288% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0249%

Overall 0.00396% 64/1,614,228 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.04%	2,502
Admixed American	0.0167%	6,003
East Asian	0.00891%	11,223
South Asian	0.0022%	45,545
Remaining individualsnot grpmax-eligible	0.0016%	62,512
European (non-Finnish)	0.00144%	69,414

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: DPT
Protein: p.Val59Met
Coding: c.175G>A
MANE Select: NM_001937
dbSNP: rs146462912
Type: single nucleotide variant
Location: chr1:168729000 (GRCh38)
Gene constraint: LOEUF 0.963 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.21
Residue 59: a disulfide bond; the '2 x 53-55 aa tandem repeats' region

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

Similar variants

DPT p.Ala58= Benign ★★ same type
DPT p.Phe130= Likely benign ★★ same type
DPT p.Ser83Ile Likely benign ★★ same type
DPT p.Tyr194= Benign ★★ same type
DPT p.Val201Ile Benign ★★ same type
DPT p.Arg126Gln Uncertain significance ★ ⚠ same type
DPT p.Arg134Cys Uncertain significance ★ ⚠ same type
DPT p.Arg134His 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/dpt-p-val59met (accessed [today's date]).

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