Is PDCD6IP p.Pro802His (c.2405C>A) pathogenic?

PDCD6IP p.Pro802His (c.2405C>A) is classified Uncertain significance in PDCD6IP (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-27). AlphaMissense: ambiguous (0.5489); Absent from gnomAD v4.1.

How common is PDCD6IP p.Pro802His (c.2405C>A) in the general population?

PDCD6IP p.Pro802His (c.2405C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PDCD6IP p.Pro802His (c.2405C>A)?

AlphaMissense predicts ambiguous (score 0.5489) — an in-silico prediction, not a clinical call.

PDCD6IP p.Pro802His

c.2405C>A · rs2491606698 · VCV2313915

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5489 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.5489	ambiguous
REVEL	0.246	benign-leaning
SaProt	LLR -8.44	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.8, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 2,508 bp · p 0.82 · regional, not allelic
Overall
CADD	27.2	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PDCD6IP
Protein: p.Pro802His
Coding: c.2405C>A
MANE Select: NM_013374
dbSNP: rs2491606698
Type: single nucleotide variant
Location: chr3:33865403 (GRCh38)
Gene constraint: LOEUF 0.583 · pLI 0.19 (gnomAD)
Structure: AlphaFold pLDDT 84.16 · 19 PDB
Residue 802: a β-strand; the 'interaction with eiav p9' region; the 'interaction with sdcbp' region; the 'self-association' region; the 'disordered' region; the 'interaction with cep55' region

Full PDCD6IP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PDCD6IP p.Ala726= Likely benign ★★ same type
PDCD6IP p.Gly429Ser Benign ★★ ⚠ same type
PDCD6IP p.Gly778Ala Benign ★★ same type
PDCD6IP p.Pro749= Benign ★★ same type
PDCD6IP p.Thr789= Benign ★★ same type
PDCD6IP p.Ala657Val Uncertain significance ★ ⚠ same type
PDCD6IP p.Ala719Thr Conflicting classifications of pathogenicity ★ ⚠ same type
PDCD6IP p.Ala726Val 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/pdcd6ip-p-pro802his (accessed [today's date]).

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