Is IDS p.Phe78= (c.234T>C) pathogenic?

IDS p.Phe78= (c.234T>C) is classified Benign/Likely benign in IDS (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-20). Ultra-rare (popmax 0.0328%, amr); Associated with Inborn genetic diseases.

What condition is associated with IDS p.Phe78= (c.234T>C)?

IDS p.Phe78= (c.234T>C) is associated with Inborn genetic diseases, mucopolysaccharidosis type 3A, mucopolysaccharidosis type 2 (ClinVar).

How common is IDS p.Phe78= (c.234T>C) in the general population?

IDS p.Phe78= (c.234T>C) is ultra-rare (popmax 0.0328%, amr) (gnomAD).

IDS p.Phe78=

c.234T>C · rs782290556 · VCV707989

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0328%, amr)

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 5.1	GERP 0.36, phastCons 1
Overall
CADD	11.26	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0328% Admixed American · 15/45,674 alleles

Filtering AF 0.0202% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0163%

Overall 0.0029% 35/1,206,845 alleles · ultra-rare exomes 27/1,094,456 · genomes 8/112,389 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0328%	3,045
Ashkenazi Jewishnot grpmax-eligible	0.0319%	3,134
Remaining individualsnot grpmax-eligible	0.00843%	11,868
African / African-American	0.00175%	57,219
European (non-Finnish)	0.000896%	111,621

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: IDS
Protein: p.Phe78=
Coding: c.234T>C
MANE Select: NM_000202
dbSNP: rs782290556
Type: single nucleotide variant
Location: chrX:149504163 (GRCh38)
Structure: AlphaFold pLDDT 93.39 · 2 PDB
Residue 78: a β-strand

Full IDS 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: mucopolysaccharidosis type 3A mucopolysaccharidosis type 2

Similar variants

IDS p.Phe78_Ala79del Pathogenic ★ same residue
IDS c.1006+1G>C Pathogenic ★★ same condition
IDS c.1006+1G>T Pathogenic ★★ same condition
IDS c.1007-133A>G Likely pathogenic ★★ same condition
IDS c.1007-1G>A Pathogenic ★★ same condition
IDS c.1007-2A>C Pathogenic/Likely pathogenic ★★ same condition
IDS c.1007-8T>G Pathogenic/Likely pathogenic ★★ same condition
IDS c.103+1G>A 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/ids-p-phe78 (accessed [today's date]).

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