Is INPP5E p.Ser205Pro (c.613T>C) pathogenic?

INPP5E p.Ser205Pro (c.613T>C) is classified Uncertain significance in INPP5E (ClinVar, Single submitter, 1 submitter; last evaluated 2020-12-04). AlphaMissense: likely benign (0.1151); Absent from gnomAD v4.1; Associated with Joubert syndrome.

What condition is associated with INPP5E p.Ser205Pro (c.613T>C)?

INPP5E p.Ser205Pro (c.613T>C) is associated with Joubert syndrome (ClinVar).

How common is INPP5E p.Ser205Pro (c.613T>C) in the general population?

INPP5E p.Ser205Pro (c.613T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about INPP5E p.Ser205Pro (c.613T>C)?

AlphaMissense predicts likely benign (score 0.1151) — an in-silico prediction, not a clinical call.

INPP5E p.Ser205Pro

c.613T>C · rs1216505048 · VCV1395429

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1151 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Joubert syndrome

Computational evidence

Protein change
AlphaMissense	0.1151	likely benign
REVEL	0.493	indeterminate
SaProt	LLR -6.76	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.25	GERP -2
Overall
CADD	11.37	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

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: INPP5E
Protein: p.Ser205Pro
Coding: c.613T>C
MANE Select: NM_019892
dbSNP: rs1216505048
Type: single nucleotide variant
Location: chr9:136438807 (GRCh38)
Structure: AlphaFold pLDDT 88.46

Full INPP5E gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Joubert syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

INPP5E p.Ser205= Likely benign ★ same residue
INPP5E p.Arg378Cys Pathogenic/Likely pathogenic ★★ same condition
INPP5E p.Arg435Gln Pathogenic/Likely pathogenic ★★ same condition
INPP5E p.Arg435Trp Pathogenic/Likely pathogenic ★★ same condition
INPP5E p.Arg557His Pathogenic/Likely pathogenic ★★ same condition
INPP5E p.Arg585Cys Pathogenic/Likely pathogenic ★★ same condition
INPP5E p.Arg621Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
INPP5E p.Arg621Trp Pathogenic/Likely pathogenic ★★ same condition

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/inpp5e-p-ser205pro (accessed [today's date]).

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