Is MID1 p.Pro485fs (c.1454del) pathogenic?

MID1 p.Pro485fs (c.1454del) is classified Likely pathogenic in MID1 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-11-01). No gnomAD frequency available for this variant; Associated with X-linked Opitz G/BBB syndrome.

What condition is associated with MID1 p.Pro485fs (c.1454del)?

MID1 p.Pro485fs (c.1454del) is associated with X-linked Opitz G/BBB syndrome (ClinVar).

How common is MID1 p.Pro485fs (c.1454del) in the general population?

MID1 p.Pro485fs (c.1454del) is no gnomAD frequency available for this variant (gnomAD).

MID1 p.Pro485fs

c.1454del · rs1556003200 · VCV547524

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

X-linked Opitz G/BBB syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 9 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.7	GERP -3.9

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MID1
Protein: p.Pro485fs
Coding: c.1454del
MANE Select: NM_000381
dbSNP: rs1556003200
Type: Deletion
Location: chrX:10455071 (GRCh38)
Structure: AlphaFold pLDDT 86.51 · 5 PDB
Residue 485: the b30.2/spry domain; the 'disordered' region

Full MID1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

X-linked Opitz G/BBB syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MID1 p.Ala127fs Likely pathogenic ★ same condition
MID1 p.Arg308fs Likely pathogenic ★ same condition
MID1 p.Cys392fs Likely pathogenic ★ same condition
MID1 p.Ile162fs Likely pathogenic ★ same condition
MID1 p.Thr640fs Pathogenic same condition
MID1 p.Ala130Thr Pathogenic/Likely pathogenic ★★ same condition
MID1 p.Arg277Ter Pathogenic ★★ same condition
MID1 p.Arg368Ter 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/mid1-p-pro485fs (accessed [today's date]).

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