Is GPATCH11 p.Tyr131Ter (c.393C>G) pathogenic?

GPATCH11 p.Tyr131Ter (c.393C>G) is classified Pathogenic in GPATCH11 (ClinVar, No assertion criteria, 1 submitter). Absent from gnomAD v4.1; Associated with Early onset and severe retinal dystrophy with neurological impairment and facial dysmorphia.

How common is GPATCH11 p.Tyr131Ter (c.393C>G) in the general population?

GPATCH11 p.Tyr131Ter (c.393C>G) is absent from gnomAD v4.1 (gnomAD).

GPATCH11 p.Tyr131Ter

Q: What condition is associated with GPATCH11 p.Tyr131Ter (c.393C>G)?

GPATCH11 p.Tyr131Ter (c.393C>G) is associated with Early onset and severe retinal dystrophy with neurological impairment and facial dysmorphia (ClinVar).

c.393C>G · rs2466837412 · VCV3062158

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Early onset and severe retinal dystrophy with neurological impairment and facial dysmorphia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 5 of 9
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.22	GERP -0.21, phastCons 0.97
Overall
CADD	35.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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: GPATCH11
Protein: p.Tyr131Ter
Coding: c.393C>G
MANE Select: NM_174931
dbSNP: rs2466837412
Type: single nucleotide variant
Location: chr2:37091980 (GRCh38)
Gene constraint: LOEUF 1.008 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.60
Residue 131: the g-patch domain

Full GPATCH11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Early onset and severe retinal dystrophy with neurological impairment and facial dysmorphia

Similar variants

GPATCH11 c.328+1G>T Pathogenic same condition
GPATCH11 c.449+1G>C Pathogenic same condition
GPATCH11 p.Arg152Ter Pathogenic same condition
GPATCH11 p.Ala146Ser Uncertain significance ★ ⚠ same type
GPATCH11 p.Ala36Val Uncertain significance ★ ⚠ same type
GPATCH11 p.Ala46Val Uncertain significance ★ ⚠ same type
GPATCH11 p.Arg152Gln Uncertain significance ★ ⚠ same type
GPATCH11 p.Asn75Lys 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/gpatch11-p-tyr131ter (accessed [today's date]).

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