Is MBD5 p.Ser790= (c.2370C>T) pathogenic?

MBD5 p.Ser790= (c.2370C>T) is classified Likely benign in MBD5 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-04-01). Ultra-rare (popmax 0.0164%, mid); Associated with intellectual disability, autosomal dominant 1.

What condition is associated with MBD5 p.Ser790= (c.2370C>T)?

MBD5 p.Ser790= (c.2370C>T) is associated with intellectual disability, autosomal dominant 1 (ClinVar).

How common is MBD5 p.Ser790= (c.2370C>T) in the general population?

MBD5 p.Ser790= (c.2370C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

MBD5 p.Ser790=

c.2370C>T · rs376037852 · VCV435821

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Conditions

intellectual disability, autosomal dominant 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.054	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.38	GERP 1.1, phastCons 0.99
Overall
CADD	11.98	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,080 alleles

Filtering AF 0.00286% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00195%

Overall 0.00266% 43/1,613,774 alleles · ultra-rare exomes 38/1,461,696 · genomes 5/152,078 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,080
African / African-American	0.00668%	14,976
South Asian	0.00659%	15,179
Admixed American	0.005%	19,994
European (non-Finnish)	0.00229%	43,700
Remaining individualsnot grpmax-eligible	0.0016%	62,466

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: MBD5
Protein: p.Ser790=
Coding: c.2370C>T
MANE Select: NM_001378120
dbSNP: rs376037852
Type: single nucleotide variant
Location: chr2:148470313 (GRCh38)
Gene constraint: LOEUF 0.161 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.20

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.Ser790Arg Likely benign ★ ⚠ same residue
MBD5 c.397+1G>A Pathogenic ★★ same condition
MBD5 c.397+2T>C Pathogenic ★★ same condition
MBD5 p.Arg1440Ter Pathogenic ★★ same condition
MBD5 p.Arg200Ter Pathogenic ★★ same condition
MBD5 p.Arg325Ter Pathogenic/Likely pathogenic ★★ same condition
MBD5 p.Cys60Ter Pathogenic ★★ same condition
MBD5 p.Gln587Ter 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-ser790 (accessed [today's date]).

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