Is DMP1 p.Ser293= (c.879T>C) pathogenic?

DMP1 p.Ser293= (c.879T>C) is classified Conflicting classifications of pathogenicity in DMP1 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-01-27). Rare (popmax 0.469%, nfe); Associated with hypophosphatemic rickets, autosomal recessive, 1.

What condition is associated with DMP1 p.Ser293= (c.879T>C)?

DMP1 p.Ser293= (c.879T>C) is associated with hypophosphatemic rickets, autosomal recessive, 1 (ClinVar).

How common is DMP1 p.Ser293= (c.879T>C) in the general population?

DMP1 p.Ser293= (c.879T>C) is rare (popmax 0.469%, nfe) (gnomAD).

How is Autosomal recessive hypophosphatemic rickets inherited?

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

DMP1 p.Ser293=

c.879T>C · rs150896376 · VCV198171

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.469%, nfe)

Conditions

hypophosphatemic rickets, autosomal recessive, 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 -0.5	GERP -0.95, phastCons 0.13
Overall
CADD	1.25	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.469% European (non-Finnish) · 5,532/1,179,772 alleles

Filtering AF 0.459% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.454%

Overall 0.37% 5,973/1,613,070 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.469%	213
Remaining individualsnot grpmax-eligible	0.23%	434
Amishnot grpmax-eligible	0.22%	455
Admixed American	0.16%	624
Middle Eastern	0.116%	866
South Asian	0.0857%	1,167
African / African-American	0.0831%	1,203
Finnishnot grpmax-eligible	0.0564%	1,773
Ashkenazi Jewishnot grpmax-eligible	0.0541%	1,850

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: DMP1
Protein: p.Ser293=
Coding: c.879T>C
MANE Select: NM_004407
dbSNP: rs150896376
Type: single nucleotide variant
Location: chr4:87662657 (GRCh38)
Gene constraint: LOEUF 1.209 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 47.80
Residue 293: the 'disordered' region

Full DMP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hypophosphatemic rickets, autosomal recessive, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal recessive hypophosphatemic rickets (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy

Similar variants

DMP1 p.Gly135Ter Pathogenic/Likely pathogenic ★★ same condition
DMP1 p.Met1Val Pathogenic/Likely pathogenic ★★ same condition
DMP1 c.*159T>A Uncertain significance ★★ same condition
DMP1 c.*77T>C Uncertain significance ★★ same condition
DMP1 p.Arg173Trp Uncertain significance ★★ ⚠ same condition
DMP1 p.Arg302Ile Uncertain significance ★★ ⚠ same condition
DMP1 p.Asn233Lys Uncertain significance ★★ ⚠ same condition
DMP1 p.Asn332Lys 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/dmp1-p-ser293 (accessed [today's date]).

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