Is MBD5 p.Pro342Thr (c.1023_1024delinsGA) pathogenic?

MBD5 p.Pro342Thr (c.10231024delinsGA) is classified Pathogenic in MBD5 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-05-02). No gnomAD frequency available for this variant; Associated with intellectual disability, autosomal dominant 1.

What condition is associated with MBD5 p.Pro342Thr (c.1023_1024delinsGA)?

MBD5 p.Pro342Thr (c.1023_1024delinsGA) is associated with intellectual disability, autosomal dominant 1 (ClinVar).

How common is MBD5 p.Pro342Thr (c.1023_1024delinsGA) in the general population?

MBD5 p.Pro342Thr (c.1023_1024delinsGA) is no gnomAD frequency available for this variant (gnomAD).

MBD5 p.Pro342Thr

c.1023_1024delinsGA · rs2469860236 · VCV1710256

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

intellectual disability, autosomal dominant 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.5	GERP 0.039, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 27 kb · p 0.0029 · regional, not allelic

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: MBD5
Protein: p.Pro342Thr
Coding: c.1023_1024delinsGA
MANE Select: NM_001378120
dbSNP: rs2469860236
Type: Indel
Location: chr2:148468966 (GRCh38)
Gene constraint: LOEUF 0.161 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.20
Residue 342: the 'disordered' region

Full MBD5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability, autosomal dominant 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MBD5 p.Pro342del Uncertain significance ★★ same residue
MBD5 p.Pro342His Uncertain significance ★★ ⚠ same residue
MBD5 p.Arg180_Leu181delinsSerIle Uncertain significance ★ same condition
MBD5 p.Gly1312Val Uncertain significance ★ same condition
MBD5 p.His1478Asn Conflicting classifications of pathogenicity ★ same condition
MBD5 p.Met708_Ser709delinsIleCys Uncertain significance ★ same condition
MBD5 c.397+1G>A Pathogenic ★★ same condition
MBD5 c.397+2T>C 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/mbd5-p-pro342thr (accessed [today's date]).

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