Is DNPH1 p.Ser10Arg (c.30C>A) pathogenic?

DNPH1 p.Ser10Arg (c.30C>A) is classified Uncertain significance in DNPH1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-05). AlphaMissense: likely benign (0.0867); Absent from gnomAD v4.1.

How common is DNPH1 p.Ser10Arg (c.30C>A) in the general population?

DNPH1 p.Ser10Arg (c.30C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DNPH1 p.Ser10Arg (c.30C>A)?

AlphaMissense predicts likely benign (score 0.0867) — an in-silico prediction, not a clinical call.

DNPH1 p.Ser10Arg

c.30C>A · rs2533987526 · VCV2556530

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0867 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,400,302)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0867	likely benign
REVEL	0.05	moderately benign-leaning
SaProt	LLR -5.84	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 -0.14	GERP -3.2
Regional constraint	o/e 1.03	unconstrained · MANE · 3,720 bp · p 0.67 · regional, not allelic
Overall
CADD	8.783	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 1,400,302). 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: DNPH1
Protein: p.Ser10Arg
Coding: c.30C>A
MANE Select: NM_006443
dbSNP: rs2533987526
Type: single nucleotide variant
Location: chr6:43229427 (GRCh38)
Gene constraint: LOEUF 1.914 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.50 · 25 PDB

Full DNPH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNPH1 p.Ala134Thr Uncertain significance ★ ⚠ same type
DNPH1 p.Ala22Thr Uncertain significance ★ ⚠ same type
DNPH1 p.Ala58Glu Uncertain significance ★ ⚠ same type
DNPH1 p.Ala69Pro Uncertain significance ★ ⚠ same type
DNPH1 p.Ala87Val Uncertain significance ★ same type
DNPH1 p.Arg125His Uncertain significance ★ ⚠ same type
DNPH1 p.Arg132Gly Uncertain significance ★ same type
DNPH1 p.Arg132Trp 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/dnph1-p-ser10arg (accessed [today's date]).

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