Is GLIS2 p.Phe421Ser (c.1262T>C) pathogenic?

GLIS2 p.Phe421Ser (c.1262T>C) is classified Uncertain significance in GLIS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-28). AlphaMissense: ambiguous (0.5497); Very rare (popmax 0.00811%, nfe); Associated with nephronophthisis 7.

What condition is associated with GLIS2 p.Phe421Ser (c.1262T>C)?

GLIS2 p.Phe421Ser (c.1262T>C) is associated with nephronophthisis 7 (ClinVar).

How common is GLIS2 p.Phe421Ser (c.1262T>C) in the general population?

GLIS2 p.Phe421Ser (c.1262T>C) is very rare (popmax 0.00811%, nfe) (gnomAD).

How is Nephronophthisis inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about GLIS2 p.Phe421Ser (c.1262T>C)?

AlphaMissense predicts ambiguous (score 0.5497) — an in-silico prediction, not a clinical call.

GLIS2 p.Phe421Ser

c.1262T>C · VCV3580721

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5497 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00811%, nfe)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

nephronophthisis 7

Computational evidence

Protein change
AlphaMissense	0.5497	ambiguous
REVEL	0.117	moderately benign-leaning
SaProt	LLR -6.05	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 7.8	GERP 1.8, phastCons 1
Regional constraint	o/e 1.12	unconstrained · MANE · 624 bp · p 0.045 · regional, not allelic
Overall
CADD	23.5	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 0.00811% European (non-Finnish) · 93/1,147,052 alleles

Filtering AF 0.00675% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00626%

Overall 0.00601% 93/1,547,518 alleles · very rare

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: GLIS2
Protein: p.Phe421Ser
Coding: c.1262T>C
MANE Select: NM_032575
Type: single nucleotide variant
Location: chr16:4337211 (GRCh38)
Gene constraint: LOEUF 0.637 · pLI 0.33 (gnomAD)
Structure: AlphaFold pLDDT 55.47

Full GLIS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

nephronophthisis 7 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Nephronophthisis (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Antenatal, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Finland)

Similar variants

GLIS2 p.Phe421Tyr Uncertain significance ★ ⚠ same residue
GLIS2 c.*1826C>T Uncertain significance ★★ same condition
GLIS2 c.*916G>A Uncertain significance ★★ same condition
GLIS2 p.Ala19Val Uncertain significance ★★ ⚠ same condition
GLIS2 p.Ala210Thr Uncertain significance ★★ same condition
GLIS2 p.Ala437Thr Uncertain significance ★★ ⚠ same condition
GLIS2 p.Arg24Gln Uncertain significance ★★ ⚠ same condition
GLIS2 p.Arg332His Uncertain significance ★★ ⚠ 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/glis2-p-phe421ser (accessed [today's date]).

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