Is SMS p.Pro113= (c.339C>T) pathogenic?

SMS p.Pro113= (c.339C>T) is classified Likely benign in SMS (ClinVar, Single submitter, 1 submitter; last evaluated 2019-03-10). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with SMS p.Pro113= (c.339C>T)?

SMS p.Pro113= (c.339C>T) is associated with Inborn genetic diseases (ClinVar).

How common is SMS p.Pro113= (c.339C>T) in the general population?

SMS p.Pro113= (c.339C>T) is absent from gnomAD v4.1 (gnomAD).

SMS p.Pro113=

c.339C>T · rs2519669219 · VCV1730981

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.1	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP 0.39, phastCons 1
Overall
CADD	12.77	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SMS
Protein: p.Pro113=
Coding: c.339C>T
MANE Select: NM_004595
dbSNP: rs2519669219
Type: single nucleotide variant
Location: chrX:21977070 (GRCh38)
Structure: AlphaFold pLDDT 95.09 · 2 PDB
Residue 113: an α-helix

Full SMS 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

Similar variants

SMS p.Pro113Ser Uncertain significance ★ ⚠ same residue
SMS p.Arg234Ter Pathogenic/Likely pathogenic ★★ same condition
SMS p.Gly56Ser Pathogenic ★★ ⚠ same condition
SMS p.Pro112Leu Pathogenic/Likely pathogenic ★★ ⚠ same condition
SMS p.Lys245Asn Uncertain significance ★★ ⚠ same condition
SMS p.Ser184Asn Uncertain significance ★★ ⚠ same condition
SMS p.Ala36Val Likely benign ★★ same condition
SMS p.Glu187= Benign/Likely benign ★★ 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/sms-p-pro113 (accessed [today's date]).

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