Is IQSEC2 p.Pro1310= (c.3930C>T) pathogenic?

IQSEC2 p.Pro1310= (c.3930C>T) is classified Likely benign in IQSEC2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-08-02). Very rare (popmax 0.00447%, nfe); Associated with intellectual disability, X-linked 1.

What condition is associated with IQSEC2 p.Pro1310= (c.3930C>T)?

IQSEC2 p.Pro1310= (c.3930C>T) is associated with intellectual disability, X-linked 1 (ClinVar).

How common is IQSEC2 p.Pro1310= (c.3930C>T) in the general population?

IQSEC2 p.Pro1310= (c.3930C>T) is very rare (popmax 0.00447%, nfe) (gnomAD).

IQSEC2 p.Pro1310=

Q: How is Severe intellectual disability-progressive postnatal microcephaly-midline stereotypic hand movements syndrome inherited?

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

c.3930C>T · rs913156254 · VCV1662532

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00447%, nfe)

Conditions

intellectual disability, X-linked 1

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 -0.61	GERP -2.8, phastCons 0.002
Overall
CADD	3.436	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00447% European (non-Finnish) · 38/849,779 alleles

Filtering AF 0.00332% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00291%

Overall 0.00349% 39/1,118,490 alleles · very rare exomes 37/1,011,135 · genomes 2/107,355 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00447%	22,363
East Asian	0.00331%	30,167

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: IQSEC2
Protein: p.Pro1310=
Coding: c.3930C>T
MANE Select: NM_001111125
dbSNP: rs913156254
Type: single nucleotide variant
Location: chrX:53234756 (GRCh38)
Structure: AlphaFold pLDDT 54.46 · 2 PDB
Residue 1310: the 'disordered' region

Full IQSEC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability, X-linked 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Severe intellectual disability-progressive postnatal microcephaly-midline stereotypic hand movements syndrome (Orphanet):

Inheritance: X-linked recessive
Onset: Infancy, Neonatal

Similar variants

IQSEC2 c.2459+21C>T Pathogenic ★★ same condition
IQSEC2 c.2889+1G>A Pathogenic ★★ same condition
IQSEC2 p.Ala836Val Pathogenic/Likely pathogenic ★★ same condition
IQSEC2 p.Arg1055Ter Pathogenic ★★ same condition
IQSEC2 p.Arg1145Ter Pathogenic ★★ same condition
IQSEC2 p.Arg531Ter Pathogenic/Likely pathogenic ★★ same condition
IQSEC2 p.Arg758Ter Pathogenic ★★ same condition
IQSEC2 p.Arg855Ter 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/iqsec2-p-pro1310 (accessed [today's date]).

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