Is IPO11 p.Phe806Ser (c.2417T>C) pathogenic?

IPO11 p.Phe806Ser (c.2417T>C) is classified Uncertain significance in IPO11 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-02). AlphaMissense: likely pathogenic (0.7702); Ultra-rare (popmax 0.0417%, amr).

How common is IPO11 p.Phe806Ser (c.2417T>C) in the general population?

IPO11 p.Phe806Ser (c.2417T>C) is ultra-rare (popmax 0.0417%, amr) (gnomAD).

What do computational predictors say about IPO11 p.Phe806Ser (c.2417T>C)?

AlphaMissense predicts likely pathogenic (score 0.7702) — an in-silico prediction, not a clinical call.

IPO11 p.Phe806Ser

c.2417T>C · rs762667790 · VCV3110297

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7702 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0417%, amr)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.7702	likely pathogenic
REVEL	0.69	pathogenic-leaning
SaProt	LLR -8.99	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.8	GERP 1.9, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 97 kb · p 0.68 · regional, not allelic
Overall
CADD	28.0	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

Grpmax group 0.0417% Admixed American · 25/59,986 alleles

Filtering AF 0.0289% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0247%

Overall 0.00162% 26/1,609,498 alleles · ultra-rare exomes 24/1,457,340 · genomes 2/152,158 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0417%	2,399
Remaining individualsnot grpmax-eligible	0.00161%	62,260

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: IPO11
Protein: p.Phe806Ser
Coding: c.2417T>C
MANE Select: NM_016338
dbSNP: rs762667790
Type: single nucleotide variant
Location: chr5:62551293 (GRCh38)
Gene constraint: LOEUF 0.598 · pLI 0.10 (gnomAD)
Structure: AlphaFold pLDDT 93.53

Full IPO11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

IPO11 p.Thr409Ala Uncertain significance ★★ ⚠ same type
IPO11 p.Ala726= Benign ★★ same type
IPO11 p.Asn260Asp Benign ★★ same type
IPO11 p.Leu112= Benign ★★ same type
IPO11 p.Leu246= Benign ★★ same type
IPO11 p.Leu799= Benign ★★ same type
IPO11 p.Ala110Val Uncertain significance ★ ⚠ same type
IPO11 p.Ala332Thr 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/ipo11-p-phe806ser (accessed [today's date]).

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