Is SLC35D1 p.Pro17= (c.51C>A) pathogenic?

SLC35D1 p.Pro17= (c.51C>A) is classified Likely benign in SLC35D1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-17). Very rare (popmax 0.00331%, nfe); Associated with schneckenbecken dysplasia.

What condition is associated with SLC35D1 p.Pro17= (c.51C>A)?

SLC35D1 p.Pro17= (c.51C>A) is associated with schneckenbecken dysplasia (ClinVar).

How common is SLC35D1 p.Pro17= (c.51C>A) in the general population?

SLC35D1 p.Pro17= (c.51C>A) is very rare (popmax 0.00331%, nfe) (gnomAD).

SLC35D1 p.Pro17=

c.51C>A · rs373050297 · VCV2166967

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00331%, nfe)

Conditions

schneckenbecken dysplasia

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 7.9	GERP 3.4, phastCons 1
Overall
CADD	14.22	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00331% European (non-Finnish) · 39/1,179,638 alleles

Filtering AF 0.00247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00217%

Overall 0.00248% 40/1,613,466 alleles · very rare exomes 37/1,461,262 · genomes 3/152,204 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00331%	30,247
Remaining individualsnot grpmax-eligible	0.0016%	62,448

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: SLC35D1
Protein: p.Pro17=
Coding: c.51C>A
MANE Select: NM_015139
dbSNP: rs373050297
Type: single nucleotide variant
Location: chr1:67053963 (GRCh38)
Gene constraint: LOEUF 0.981 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 80.98
Residue 17: the 'disordered' region

Full SLC35D1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

schneckenbecken dysplasia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SLC35D1 p.Pro17Leu Uncertain significance ★ ⚠ same residue
SLC35D1 p.Ala343Val Uncertain significance ★★ ⚠ same condition
SLC35D1 p.Gly202Ala Uncertain significance ★★ same condition
SLC35D1 p.Gly47Ser Uncertain significance ★★ ⚠ same condition
SLC35D1 p.Leu101Phe Uncertain significance ★★ ⚠ same condition
SLC35D1 p.Lys13Glu Uncertain significance ★★ ⚠ same condition
SLC35D1 p.Met301Thr Uncertain significance ★★ ⚠ same condition
SLC35D1 p.Pro70Ser Uncertain significance ★★ ⚠ 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/slc35d1-p-pro17 (accessed [today's date]).

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