Is DPT p.Arg138= (c.414G>A) pathogenic?

DPT p.Arg138= (c.414G>A) is classified Likely benign in DPT (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-09). Common (popmax 7.27%, sas) — too common for a highly-penetrant pathogenic allele.

DPT p.Arg138=

Q: How common is DPT p.Arg138= (c.414G>A) in the general population?

DPT p.Arg138= (c.414G>A) is common (popmax 7.27%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.414G>A · VCV3273675

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 7.27%, sas) — too common for a highly-penetrant pathogenic allele

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 -1.1	GERP -4.7, phastCons 0.002
Overall
CADD	2.411	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.27% South Asian · 6,625/91,070 alleles

Filtering AF 7.13% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.07%

Overall 5.69% 91,881/1,614,010 alleles · common

Ancestry group	Frequency	1 in
South Asiangrpmax	7.27%	14
European (non-Finnish)	6.41%	16
Remaining individualsnot grpmax-eligible	5.39%	19
Middle Eastern	5.34%	19
Finnishnot grpmax-eligible	3.9%	26
Ashkenazi Jewishnot grpmax-eligible	3.82%	26
Admixed American	2.49%	40
Amishnot grpmax-eligible	1.43%	70
African / African-American	0.981%	102
East Asian	0.0223%	4,487

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.Arg138=
Coding: c.414G>A
MANE Select: NM_001937
Type: single nucleotide variant
Location: chr1:168714238 (GRCh38)
Gene constraint: LOEUF 0.963 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.21
Residue 138: the '2 x 53-55 aa tandem repeats' region; the '3 x 6 aa repeats of d-r-[eq]-w-[nqk]-[fy]' 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-arg138 (accessed [today's date]).

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