# NM_014489.4(PGAP2):c.449T>C (p.Phe150Ser)

https://sugi.bio/variant/pgap2-p-phe150ser

## Summary

**PGAP2 p.Phe150Ser (c.449T>C)** is classified **Likely pathogenic** in PGAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-05-28). AlphaMissense: likely pathogenic (0.969); Absent from gnomAD v4.1; Associated with hyperphosphatasia with intellectual disability syndrome 3.

**At a glance:** Likely pathogenic · review: Single submitter · rsID rs1590416370 · 1 submitter · 1 linked condition · AlphaMissense likely pathogenic · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the PGAP2 gene that is considered likely disease-causing, submitted by 1 submitter, and is linked to hyperphosphatasia with intellectual disability syndrome 3.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | Infancy, Neonatal |
| Diagnostic panels | PGAP2 is a diagnostic-grade gene on 11 Genomics England panels |

**Commonly reported features of Hyperphosphatasia-intellectual disability syndrome** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Hypertelorism — Very frequent (99-80%)
- Seizure — Very frequent (99-80%)
- Global developmental delay — Very frequent (99-80%)
- Elevated circulating alkaline phosphatase concentration — Very frequent (99-80%)
- Shortening of all distal phalanges of the fingers — Very frequent (99-80%)
- Floppy infant — Very frequent (99-80%)
- Wide nasal bridge — Frequent (79-30%)
- Long palpebral fissure — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0018350/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PGAP2](https://sugi.bio/atlas/gene/PGAP2/) |
| Protein change (HGVS p.) | p.Phe150Ser |
| Coding change (HGVS c.) | c.449T>C |
| MANE Select transcript | [NM_014489](https://www.ncbi.nlm.nih.gov/nuccore/NM_014489) |
| dbSNP | [rs1590416370](https://www.ncbi.nlm.nih.gov/snp/rs1590416370/) |
| Variant type | single nucleotide variant |
| Location | chr11:3823983-3823983 (GRCh38) |
| ClinVar | [VCV802653](https://www.ncbi.nlm.nih.gov/clinvar/variation/802653/) |

**All HGVS expressions:** `NC_000011.10:g.3823983T>C`, `NC_000011.9:g.3845213T>C`, `NG_051812.1:g.31260T>C`, `NM_001145438.3:c.266T>C`, `NM_001256235.2:c.320T>C`, `NM_001256236.2:c.449T>C`, `NM_001256237.2:c.266T>C`, `NM_001256238.2:c.266T>C`, `NM_001256239.2:c.266T>C`, `NM_001256240.2:c.266T>C`, `NM_001283038.2:c.266T>C`, `NM_001283039.2:c.189T>C`, `NM_001283040.1:c.162-287T>C`, `NM_001346397.2:c.419T>C`, `NM_001346398.2:c.266T>C`, `NM_001346399.2:c.276T>C`, `NM_001346400.2:c.266T>C`, `NM_001346401.2:c.276T>C`, `NM_001346402.2:c.386T>C`, `NM_001346403.1:c.449T>C`, `NM_001346404.1:c.266T>C`, `NM_001346405.1:c.266T>C`, `NM_014489.4:c.449T>C`, `NR_027016.3:n.193T>C`, `NR_027017.4:n.586T>C`, `NR_027018.2:n.414T>C`, `NR_045923.2:n.208T>C`, `NR_045927.2:n.208T>C`, `NR_045929.2:n.321T>C`, `NR_104270.2:n.208T>C`, `NR_104271.2:n.468T>C`, `NR_104272.2:n.193T>C`, `NR_144427.2:n.208T>C`, `NR_144428.2:n.453T>C`, `NR_144429.2:n.193T>C`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- AlphaMissense **likely pathogenic** (0.969) — concordant with the pathogenic call
- REVEL 0.55 (indeterminate)
- SaProt LLR -13.032 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and SaProt both call this damaging; REVEL is indeterminate
- Conservation: phyloP 7.898, GERP 1.84, phastCons 1 — highly conserved (agrees)
- ⚠ **Isoform check:** AlphaMissense is numbered on a different transcript (AM **F89S** vs ClinVar **F150S**) — the AlphaMissense read here may be for a different residue; verify against the ClinVar transcript.
- CADD: **PHRED 30.0**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- Regional missense constraint: **o/e 0.88** across the covering region of the MANE Select transcript (3,811,422–3,825,455), spanning 14,033 bp. Chi-square p 0.023. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **no splice effect predicted**. SpliceAI outputs four numbers per variant, not one: acceptor loss, donor loss, acceptor gain, donor gain (DS_AL / DS_DL / DS_AG / DS_DG). A loss score is an existing splice site weakened or destroyed; a gain score is a new site created or an existing one strengthened. The release publishes its own filter rule, which we read from the dataset rather than assume: an allele is reported only if the largest of its four deltas reaches 0.2. No allele at this position is in the release, so all four are under 0.2 for every alternate allele here. No figure is shown because none was read: the bound is deduced from that absence. It is a result, not a gap in our data, because the release scores every possible substitution across the transcripts it covers (Ensembl MANE v1.4) before it filters, so what survives for a gene is one continuous stretch. What is measured is that this position sits inside the stretch covered for PGAP2 (510 scored positions, the nearest 3 bases away); what is taken from the release's own description, rather than measured, is that coverage inside that stretch is continuous. On that, SpliceAI did score it. *ClinGen's SVI treats the largest of the four as evidence against a splicing effect at or below 0.1, where it may support BP4, and as uninformative between 0.1 and 0.2. We cannot tell which applies here, so these SpliceAI data support neither BP4 nor PP3; that is a statement about this evidence alone, not about the variant's other evidence.*
- Population frequency: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**PGAP2** population constraint: LOEUF 0.871, pLI 0.00010679, missense-Z 1.6257. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 90.00, 73% of residues very-high.

## Clinical significance {#significance}

**Likely pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2019-05-28.

**Submitter consensus:** unanimous (1/1 Likely pathogenic).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Mendelics | Likely pathogenic | criteria provided, single submitter | clinical testing | 2019-05-28 |

## Associated conditions {#conditions}

[hyperphosphatasia with intellectual disability syndrome 3](https://sugi.bio/atlas/disease/hyperphosphatasia-with-intellectual-disability-syndrome-3/).

**Reported phenotype names (ClinVar):** Hyperphosphatasia with intellectual disability syndrome 3, GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 8, HYPERPHOSPHATASIA WITH IMPAIRED INTELLECTUAL DEVELOPMENT SYNDROME 3.

## Similar variants {#similar}

Related PGAP2 variant pages (same residue, condition, or type): [PGAP2 p.Ala127Val](/variant/pgap2-p-ala127val), [PGAP2 p.Arg238Pro](/variant/pgap2-p-arg238pro), [PGAP2 p.Thr294Met](/variant/pgap2-p-thr294met), [PGAP2 c.602-3C>T](/variant/pgap2-c-602-minus-3c-t), [PGAP2 p.Asn205Lys](/variant/pgap2-p-asn205lys), [PGAP2 p.Ser257Leu](/variant/pgap2-p-ser257leu), [PGAP2 c.166-1G>C](/variant/pgap2-c-166-minus-1g-c), [PGAP2 p.Arg246Gln](/variant/pgap2-p-arg246gln).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 802653). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*