Is DEPP1 p.His210Arg (c.629A>G) pathogenic?

DEPP1 p.His210Arg (c.629A>G) is classified Uncertain significance in DEPP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-14). AlphaMissense: likely benign (0.189); Absent from gnomAD v4.1.

How common is DEPP1 p.His210Arg (c.629A>G) in the general population?

DEPP1 p.His210Arg (c.629A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DEPP1 p.His210Arg (c.629A>G)?

AlphaMissense predicts likely benign (score 0.189) — an in-silico prediction, not a clinical call.

DEPP1 p.His210Arg

c.629A>G · VCV4907123

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.189 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,582,250)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.189	likely benign
REVEL	0.241	benign-leaning
SaProt	LLR -5.14	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 3.2	GERP 1.5, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 635 bp · p 0.43 · regional, not allelic
Overall
CADD	22.3	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

No allele count reported in gnomAD v4.1 (AN 1,582,250). 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: DEPP1
Protein: p.His210Arg
Coding: c.629A>G
MANE Select: NM_007021
Type: single nucleotide variant
Location: chr10:44977402 (GRCh38)
Gene constraint: LOEUF 1.774 · pLI 0.38 (gnomAD)
Structure: AlphaFold pLDDT 60.32

Full DEPP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DEPP1 p.Thr101Ala Benign ★★ same type
DEPP1 p.Ser183Phe Uncertain significance ★ ⚠ same type
DEPP1 p.Val9Met Uncertain significance ★ ⚠ same type
DEPP1 p.Arg83Gln Likely benign ★ same type
DEPP1 p.Arg88Cys Likely benign ★ 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/depp1-p-his210arg (accessed [today's date]).

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