Is MECP2 p.Ser369= (c.1107C>T) pathogenic?

MECP2 p.Ser369= (c.1107C>T) is classified Benign/Likely benign in MECP2 (ClinVar, Multiple submitters, 10 submitters; last evaluated 2025-11-12). Ultra-rare (popmax 0.0493%, sas); Associated with Inborn genetic diseases.

What condition is associated with MECP2 p.Ser369= (c.1107C>T)?

MECP2 p.Ser369= (c.1107C>T) is associated with Inborn genetic diseases, severe neonatal-onset encephalopathy with microcephaly, Rett syndrome (ClinVar).

How common is MECP2 p.Ser369= (c.1107C>T) in the general population?

MECP2 p.Ser369= (c.1107C>T) is ultra-rare (popmax 0.0493%, sas) (gnomAD).

MECP2 p.Ser369=

c.1107C>T · rs61750236 · VCV95183

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0493%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.2	GERP -1.1
Overall
CADD	1.867	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0493% South Asian · 28/56,767 alleles

Filtering AF 0.035% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0302%

Overall 0.027% 327/1,209,024 alleles · ultra-rare exomes 320/1,097,683 · genomes 7/111,341 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0493%	2,027
European (non-Finnish)	0.0305%	3,277
Middle Eastern	0.0231%	4,331
Remaining individualsnot grpmax-eligible	0.0147%	6,798
African / African-American	0.0123%	8,146
Admixed American	0.0109%	9,154
East Asian	0.00889%	11,243
Finnishnot grpmax-eligible	0.00645%	15,492

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: MECP2
Protein: p.Ser369=
Coding: c.1107C>T
MANE Select: NM_001110792
dbSNP: rs61750236
Type: single nucleotide variant
Location: chrX:154030757 (GRCh38)
Structure: AlphaFold pLDDT 57.25 · 11 PDB
Residue 369: a UniProt-annotated variant site (in rtt); the 'disordered' region

Full MECP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: severe neonatal-onset encephalopathy with microcephaly Rett syndrome

Similar variants

MECP2 p.Ser369del Uncertain significance ★★ same residue
MECP2 p.Ser369fs Pathogenic ★ same residue
MECP2 p.Ser369Gly Uncertain significance ★ ⚠ same residue
MECP2 c.414-3C>G Pathogenic ★★★ same condition
MECP2 c.62+1G>A Pathogenic ★★★ same condition
MECP2 c.62+2T>G Pathogenic ★★★ same condition
MECP2 p.Ala143Asp Pathogenic ★★★ same condition
MECP2 p.Ala291Val Likely 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/mecp2-p-ser369 (accessed [today's date]).

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